Software Search

Software Search
Software Documentation Service
Software
Resource
Containers
Description
AI Tags
AI Research Discipline
AI Software Type
Documentation, Uses, and more
abricate
lcc
1.0
Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB.
Antimicrobial Resistance, Genomic Analysis, Bacterial Genomics
Biology, Biological Sciences
Tool
Documentation, Uses, and more
absence-aware-clustering
mcc
1.0
Documentation, Uses, and more
accelerate
lcc
1.0
A simple way to launch, train, and use PyTorch models on almost any device and distributed configuration, automatic mixed precision (including fp8), and easy-to-configure FSDP and DeepSpeed support.
Machine Learning, Numerical Computing, GPU Acceleration
Machine Learning
Documentation, Uses, and more
adapterremoval
lcc
1.0
AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3’ end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.
Bioinformatics, Hts Data Processing, Sequence Analysis
Biology, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
adios
lcc
N/A
The Adaptable IO System (ADIOS)
I/O, High Performance Computing, Data Management
High Performance Computing, Scientific Data Management
Library
Documentation, Uses, and more
adios2
lcc
N/A
ADIOS2 is developed as part of the United States Department of Energy's Exascale Computing Project. It is a framework for scientific data I/O to publish and subscribe to data when and where required. ADIOS2 transports data as groups of self-describing variables and attributes across different media types (such as files, wide-area-networks, and remote direct memory access) using a common application programming interface for all transport modes. ADIOS2 can be used on supercomputers, cloud systems, and personal computers.
I/O Middleware, High-Performance Computing, Data Management, Parallel Computing
Computer Science, Computer & Information Sciences
Library
Documentation, Uses, and more
admixture
lcc, mcc
1.0
ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.
genetics, population genetics, bioinformatics
Bioinformatics, Population Genetics
Statistical Software
Documentation, Uses, and more
advisor
ecc, lcc
N/A
Intel Advisor is a performance analysis tool designed to help developers optimize and parallelize their software on Intel architectures. It provides insights for efficient vectorization, threading, and offloading to accelerators, aiding in achieving maximum performance from applications.
Hpc, Performance Optimization, Parallel Computing
Engineering & Technology
Performance Optimization
Documentation, Uses, and more
aflow
lcc
1.0
AFLOW is a comprehensive software framework for autonomous density functional theory calculations and materials properties analysis. It offers diverse tools and modules for structure analysis, property prediction, and error correction, including thermodynamic stability analysis and modeling of chemically disordered materials, with public access through the AFLOW website and search API.
Computational Software, Materials Science, Density Functional Theory
Physics & Physical Sciences, Physical Sciences
Materials Modeling & Simulation
Documentation, Uses, and more
afterqc
lcc
1.0
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair.
Quality Control, High-Throughput Sequencing Data, Next-Generation Sequencing
Biology, Biological Sciences
Application
Documentation, Uses, and more
agat
lcc
1.0
Agat is a suite of tools to handle gene annotations in any GTF/GFF format
Genome Assembly, Annotation, Evaluation, Genomic Analysis
Genomics, Biological Sciences
Pipeline
Documentation, Uses, and more
agptools
mcc
1.0
The AGP format is a tab-separated table format describing how components of a genome assembly fit together. NCBI accepts assemblies for submission in the format of a fasta file giving the sequences of components (usually contigs) along with an AGP file showing how these components are assembled into larger pieces like scaffolds or chromosomes.
Genome Assembly
Bioinformatics
Documentation, Uses, and more
alphafold3
lcc
1.0
AlphaFold 3 is an AI model from Google DeepMind and Isomorphic Labs that can predict the structure and interactions of all life’s molecules, including proteins, DNA, RNA, and small molecules (ligands). For the interactions of proteins with other molecule types it has provided least a 50% improvement compared with existing prediction methods, and for some important categories of interaction it has doubled prediction accuracy.\r
Description Source: https://blog.google/innovation-and-ai/products/google-deepmind-isomorphic-alphafold-3-ai-model/\r
Protein-Structure, Deep-Learning, Bioinformatics
Bioinformatics, Biochemistry and Molecular Biology
Predictive Modeling
Documentation, Uses, and more
amas
mcc
1.0
Documentation, Uses, and more
amber
lcc
1.0
Amber is a suite of biomolecular simulation programs together with Amber tools.
Molecular Dynamics, Biomolecular Simulations, Quantum Chemistry
Biochemistry & Molecular Biology, Biological Sciences
Molecular Dynamics
Documentation, Uses, and more
ambertools
lcc, mcc
1.0
Ambertools is a suite can of complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.
Molecular Dynamics, Computational Chemistry, Biomolecular Structure, Energy Minimization
Biophysics, Biological Sciences
Simulation Software
Documentation, Uses, and more
anaconda
lcc
1.0
Anaconda3 is a popular open-source distribution of Python and R for scientific computing, data science, and machine learning. It simplifies package management and deployment by bundling numerous libraries and tools, and it includes the conda package manager, which makes installing, running, and updating various packages and their dependencies convenient.
Data Science, Scientific Computing, Package Management, Python, R
Computer and Information Sciences
Package Management
Documentation, Uses, and more
ancestry_hmm
lcc
1.0
ancestry_hmm is a hidden Markov model–based software tool for inferring local ancestry along the genome in admixed individuals using genotype or sequencing data. It identifies ancestry transitions and ancestry proportions by modeling recombination, allele frequencies, and admixture history.
Computational genomics, Population genetics
population-genetics
Documentation, Uses, and more
angsd
lcc, mcc
1.0
Angsd is a software for analyzing next generation sequencing data.
Ngs Data Analysis, Genome-Wide Association Studies, Population Genomics, Genetic Variation
Biology, Biological Sciences
Application
Documentation, Uses, and more
annoy
lcc
1.0
Annoy (Approximate Nearest Neighbors Oh Yeah) is a high-performance library for searching large, high-dimensional vector spaces using approximate nearest-neighbor queries. It is designed for extremely fast similarity search, making it ideal for recommendation engines, clustering, retrieval, and large-scale data mining or machine-learning applications.
Machine Learning, Data Science, Approximate Nearest Neighbors, High-Dimensional Data
Machine Learning, Data Mining
Library
Documentation, Uses, and more
antismash
mcc
1.0
Antismash allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
Bioinformatics, Genome Mining, Biosynthetic Gene Clusters, Secondary Metabolites
Bioinformatics, Biological Sciences
Annotation Tool
Documentation, Uses, and more
anvio
mcc
1.0
Anvio is an analysis and visualization platform for 'omics data.
Omics Data Analysis, Microbiome, Metagenomics, Bioinformatics
Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
ape
lcc
1.0
computational chemistry, molecular dynamics, data analysis, visualization
Molecular Modeling, Molecular Dynamics
Open Source
Documentation, Uses, and more
apptainer
ecc
N/A
Apptainer, formerly known as Singularity, is an open-source container platform designed to create portable and reproducible environments for scientific computing. It allows users to package applications, their dependencies, and data in a single container that can be run consistently across different computing environments.
Description Source: https://apptainer.org/
Containerization, Application Management, Devops, Software Development
Computer Science, Engineering & Technology
Development
Documentation, Uses, and more
apt-transport-https
lcc, mcc
1.0
This APT transport allows the use of repositories accessed via the HTTP Secure protocol (HTTPS), also referred to as HTTP over TLS. It is available by default since apt 1.5 and was available before that in the package apt-transport-https. Note that a transport is never called directly by a user but used by APT tools based on user configuration.
Package Management, Security, Debian, APT
Software Systems Engineering, System Administration
System Utility
Documentation, Uses, and more
argweaver
mcc
1.0
The ARGweaver software package contains programs and libraries for sampling and manipulating ancestral recombination graphs (ARGs). An ARG is a rich data structure for representing the ancestry of DNA sequences undergoing coalescence and recombination.
bioinformatics, genetics, population genetics, software tool
Computational Evolutionary Biology, Bioinformatics
Command-line tool
Documentation, Uses, and more
armadillo
lcc
1.0
Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use. It provides high-level syntax and functionality deliberately similar to Matlab.
Description Source: https://arma.sourceforge.net/
Linear Algebra, C++ Library
Computer Science, Computer & Information Sciences
Linear Algebra Library
Documentation, Uses, and more
armadillo-devel
lcc
1.0
Armadillo is a high-quality linear algebra library for the C++ language, providing efficient operations for matrix and vector computations.
C++, Linear Algebra, Matrix Operations, Scientific Computing
Applied Mathematics, Mathematics
Library
Documentation, Uses, and more
arpack-devel
lcc
1.0
arpack-devel is a subroutine of ARPACK which is a collection of Fortran 77 subroutines designed to solve large scale eigenvalue problems. This package contains the so library links used for building arpack based applications.
Eigenvalue, Numerical Linear Algebra, High-Performance Computing
Applied Mathematics, Numerical Linear Algebra
Library
Documentation, Uses, and more
ase
lcc
1.0
ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations.
Description Source: https://wiki.fysik.dtu.dk/ase/index.html
Computational Software, Python Library, Molecular Simulations
Chemistry, Other Natural Sciences
Tool
Documentation, Uses, and more
assembly-stats
mcc
1.0
Assembly-stats is a tool to get assembly statistics from FASTA and FASTQ files.
Genome Assembly, Bioinformatics
Biology, Biological Sciences
Stand-Alone Tool
Documentation, Uses, and more
astral
mcc
1.0
ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees. ASTRAL is statistically consistent under the multi-species coalescent model (and thus is useful for handling incomplete lineage sorting, i.e., ILS). ASTRAL finds the species tree that has the maximum number of shared induced quartet trees with the set of gene trees, subject to the constraint that the set of bipartitions in the species tree comes from a predefined set of bipartitions.
Bioinformatics, Phylogenetics
Phylogenomics inference tool
Documentation, Uses, and more
atacseqqc
mcc
1.0
Documentation, Uses, and more
atomsk
lcc
1.0
Atomsk is a command-line tool for creating, manipulating, and converting atomic structures. It is widely used in materials science for generating input files for various simulation software.
atomic structures, materials science, simulation, file conversion
Computational Materials Science, Atomic and Molecular Physics
Command-line tool
Documentation, Uses, and more
augustus
lcc
1.0
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server, on a new web server for larger input files or be downloaded and run locally.
Description Source: https://bioinf.uni-greifswald.de/augustus/
Gene Prediction, Eukaryotes, Bioinformatics
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
autoconf
ecc, lcc, mcc
1.0
Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.
Build Automation, Software Configuration, Makefiles
General, Engineering & Technology
Build Tools
Documentation, Uses, and more
autoconf-archive
ecc, lcc
N/A
The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet. Every single one of those macros can be re-used without imposing any restrictions whatsoever on the licensing of the generated configure script.
Description Source: https://github.com/autoconf-archive/autoconf-archive
autoconf, macros, configuration, software development
General, Software Engineering
Service
Documentation, Uses, and more
autodock-vina
mcc
1.0
AutoDock Vina is an open-source program for doing molecular docking. AutoDock Vina is one of the docking engines of the AutoDock Suite.
Molecular Docking, Bioinformatics, Computational Chemistry, Drug Discovery
Biology, Molecular Docking
Application
Documentation, Uses, and more
automake
ecc, lcc, mcc
1.0
Automake: GNU Standards-compliant Makefile generator
Build Automation, Software Development, Compilers
General, Engineering & Technology
Compiler
Documentation, Uses, and more
autotools
ecc, lcc
N/A
This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
Programming, Software Development, Build Automation
Software Engineering, Systems & Development, Computer & Information Sciences
Build Automation
Documentation, Uses, and more
azcopy
mcc
1.0
AzCopy is a command-line utility that you can use to copy data to, from, or between storage accounts. This article helps you download AzCopy, connect to your storage account, and then transfer data.
Data Transfer, Cloud Storage, Azure, Command Line Tool
Computer Science, Data Engineering
Command Line Utility
Documentation, Uses, and more
bacmet
mcc
1.0
Documentation, Uses, and more
bader
mcc
1.0
Documentation, Uses, and more
bakta
lcc, mcc
1.0
Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. It provides dbxref-rich, sORF-including and taxon-independent annotations in machine-readable JSON & bioinformatics standard file formats for automated downstream analysis.
bacterial genome annotation, prokaryotic genomes, bioinformatics, functional annotation, gene prediction, comparative genomics, sequence analysis
Microbial genomics, Bioinformatics
Genome annotation software
Documentation, Uses, and more
bam-readcount
lcc
1.0
Bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bam-readcount/bam-readcount.html
Bioinformatics, Genomics, Variant-Calling, Coverage-Assessment
Genomics, Biological Sciences
Command Line Tool
Documentation, Uses, and more
bamtools
lcc
1.0
BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.
Description Source: https://github.com/pezmaster31/bamtools/wiki
Bioinformatics, Bam Files, Sequence Alignment, Toolkit
Biology, Biological Sciences
Toolkit
Documentation, Uses, and more
barrnap
mcc
1.0
Barrnap: Basic Rapid Ribosomal RNA Predictor. Barrnap predicts the location of ribosomal RNA genes in genomes.
Description Source: https://github.com/tseemann/barrnap
Bioinformatics, Genomics, Sequence Analysis, Ribosomal RNA, DNA Sequencing
Genomics, Biological Sciences
Sequence Analysis Tool
Documentation, Uses, and more
base
lcc, mcc
1.0
Documentation, Uses, and more
bash
ecc
N/A
Bash is a Unix shell and command language that is widely used for scripting and automation in Unix-like operating systems.
scripting, automation, command-line, Unix, Linux
Computer Science, Software Engineering
Shell
Documentation, Uses, and more
bayescan
lcc, mcc
1.0
BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bayescan/bayescan.html
Genetic Analysis, Natural Selection, Bayesian Model Comparison
Genetics, Biological Sciences
Analysis Tool
Documentation, Uses, and more
bbmap
mcc
1.0
Bbmap is a short read aligner, as well as various other bioinformatic tools.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bbmap/bbmap.html
Bioinformatics, DNA Sequencing, Sequence Alignment
Genomics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
bbmap_39.08
mcc
1.0
BBMap is a tool for aligning sequencing reads to a reference genome. It is designed for high-throughput sequencing data and can handle large datasets efficiently.
bioinformatics, genomics, sequence alignment, high-throughput sequencing
Bioinformatics, Genomics
Command-line tool
Documentation, Uses, and more
bc
ecc, lcc
1.0
bc is an arbitrary precision calculator language that supports complex mathematical operations.
Calculator, Mathematics, Command-line tool
Applied Mathematics, Other Mathematics
Command-line tool
Documentation, Uses, and more
bcbio
mcc
1.0
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel run that handles distributed execution, idempotent processing restarts and safe transactional steps. bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.
bioinformatics, genomics, high-throughput sequencing, data analysis
Computational Biology, Bioinformatics
Workflow management software
Documentation, Uses, and more
bcftools
lcc, mcc
1.0
BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF.
Description Source: https://samtools.github.io/bcftools/howtos/index.html
Variant Calling, Genomics, Bioinformatics
Genomics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
bcftools-1.11-samtools
lcc
1.0
Bcftools is a set of utilities for variant calling and manipulating VCF and BCF files. It is designed to work with SAMtools and is widely used in bioinformatics for analyzing genomic data.
bioinformatics, genomics, variant analysis
Bioinformatics, Genomics
Command-line tool
Documentation, Uses, and more
bcl2fastq2
mcc
1.0
bcl2fastq2 is a software tool used to convert BCL (Base Call) files generated by Illumina sequencing instruments into FASTQ files, which are widely used for downstream analysis in bioinformatics.
bioinformatics, genomics, sequencing
Bioinformatics, Genomics
Command-line tool
Documentation, Uses, and more
beagle
mcc
1.0
Beagle is is a software package for phasing genotypes and for imputing ungenotyped markers.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/beagle/beagle.html
Phylogenetic Inference, Maximum Likelihood, Molecular Sequence Data, Parallel Processing, Likelihood Calculations
Genetics, Biological Sciences
Library
Documentation, Uses, and more
beagle-lib
lcc, mcc
1.0
BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.
Description Source: https://github.com/beagle-dev/beagle-lib
Computational Biology, Phylogenetic Inference, Likelihood Evaluation, Evolutionary Analysis, Bioinformatics
Biology
Library
Documentation, Uses, and more
beast
mcc
1.0
BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
Description Source: https://www.beast2.org/
Bioinformatics, Computational Biology, Phylogenetics, Molecular Evolution, Bayesian Analysis
Systems Biology, Biological Sciences
Tool
Documentation, Uses, and more
beast2
lcc, mcc
1.0
BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
Description Source: https://www.beast2.org/
Phylogenetics, Evolutionary Analysis, Molecular Sequences, Bayesian Inference
Ecology, Biological Sciences
Tool
Documentation, Uses, and more
beautifulsoup4
ecc
1.0
Beautiful Soup is a library that makes it easy to scrape information from web pages. It sits atop an HTML or XML parser, providing Pythonic idioms for iterating, searching, and modifying the parse tree.
web scraping, HTML parsing, data extraction, Python
Data Science, Web Technologies
Library
Documentation, Uses, and more
bedops
lcc, mcc
1.0
BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
Description Source: https://bedops.readthedocs.io/en/latest/
Genomic Data Analysis, Bioinformatics, Computational Biology, Genomics, Data Analysis
Bioinformatics, Biological Sciences
Command-Line Tool
Documentation, Uses, and more
bedtools
lcc, mcc
1.0
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. This is an older version of bedtools2.
Description Source: https://bedtools.readthedocs.io/en/latest/
Bioinformatics, Genomics, Data Analysis, Tool
Biology, Biological Sciences
Application
Documentation, Uses, and more
berkeley-db
ecc, lcc
N/A
Berkeley DB is a family of embedded key-value database libraries providing scalable high-performance data management services to applications.
Description Source: https://docs.oracle.com/database/bdb181/
Database, Embedded Systems, High Performance, Data Management
Storage, Hpc Applications, Computer Science
Library
Documentation, Uses, and more
binutils
lcc
N/A
binutils: GNU binary utilities
Binary Tools, Linker, Assembler, Object Files
General, Computer & Information Sciences
System Software
Documentation, Uses, and more
bioawk
mcc
1.0
Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. \r
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bioawk/bioawk.html
Bioinformatics, Data Processing, File Formats, Data Analysis
Bioinformatics, Biological Sciences
Scripting Tool
Documentation, Uses, and more
biobakery_workflows
lcc
1.0
bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. Quality control and statistical summary reports are automatically generated for most data types, which include 16S amplicons, metagenomes, and metatranscriptomes. Workflows are run directly from the command line and tasks can be imported to create your own custom workflows.
bioinformatics, microbiome, data analysis, workflow
Computational Biology, Bioinformatics
Workflow Management
Documentation, Uses, and more
biocmanager
lcc
1.0
BiocManager is an R package that streamlines access to the Bioconductor ecosystem by providing reliable tools for installing, updating, and managing bioinformatics packages. It ensures that users retrieve versions compatible with their R installation, maintaining consistency and reproducibility across workflows. BiocManager also simplifies dependency resolution across both Bioconductor and CRAN, making it easier to build and maintain complex analysis environments.
R, Bioconductor, Package Management
Computational Biology, Genomics
Package Manager
Documentation, Uses, and more
bioconda
lcc, mcc
1.0
Bioconda is a specialized Conda channel that provides thousands of pre-built bioinformatics software packages, enabling fast, consistent, and reproducible installation across platforms. It streamlines software management for life-science research by simplifying dependencies and environment setup.
bioinformatics, conda, package management, software distribution
Bioinformatics, Genomics
Package Manager
Documentation, Uses, and more
bioconda::mummer4=4.0.1
lcc
1.0
MUMmer is a system for rapidly aligning entire genomes, whether they are closely related or highly divergent.
genome alignment, bioinformatics, computational biology
Bioinformatics, Biological Sciences
Command-line tool
Documentation, Uses, and more
bioconductor-atacseqqc
mcc
1.0
ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process.
ATAC-seq, Bioinformatics, Quality Control
Molecular Biology, Bioinformatics
Quality Control Tool
Documentation, Uses, and more
bioconductor-dss
lcc
1.0
DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.
bioinformatics ,methylation, genomics, Bioconductor
Bioinformatics, Molecular Biology
R package
Documentation, Uses, and more
bioconductor-lea
mcc
1.0
Documentation, Uses, and more
bioconductor-maftools
mcc
1.0
Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.
bioinformatics, cancer genomics, R package, data visualization
Cancer Research, Bioinformatics
R package
Documentation, Uses, and more
bionano
mcc
1.0
bionano OGM solutions provide the essential tools clinicians and researchers need to reveal actionable insights from all classes of genomic variations
structural variation, genome assembly, optical mapping
Molecular Biology, Life Sciences
Bioinformatics Software
Documentation, Uses, and more
biopython
lcc, mcc
1.0
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
Description Source: https://biopython.org/
Biological Computation, Bioinformatics, Computational Biology, Molecular Biology, Structural Bioinformatics
Bioinformatics, Biological Sciences
Python Library
Documentation, Uses, and more
bis-snp
mcc
1.0
BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol.
bisulfite sequencing, DNA methylation, SNP calling, epigenomics, bioinformatics, NGS analysis
Epigenomics, Bioinformatics
Variant and DNA methylation analysis software
Documentation, Uses, and more
bismark
lcc, mcc
1.0
Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away.
Description Source: https://www.bioinformatics.babraham.ac.uk/projects/bismark/
Epigenetics, DNA Methylation, Bisulfite Sequencing, Genomics, Bioinformatics
Genomics, Biological Sciences
Alignment & Methylation Analysis
Documentation, Uses, and more
bison
lcc
1.0
Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
Parser Generator, Programming Language Tool
General, Computer & Information Sciences
Parser Generator
Documentation, Uses, and more
bitsandbytes
lcc
1.0
bitsandbytes makes large language models more accessible in PyTorch by using k-bit quantization to drastically reduce memory use for both inference and training. It supports 8-bit optimizers, LLM.int8() for efficient inference with minimal performance impact, and QLoRA (4-bit) for memory-efficient training by combining 4-bit quantization with small trainable LoRA adapters.\r
Description Source: https://huggingface.co/docs/bitsandbytes/main/en/index
Deep Learning, Quantization, Memory Optimization, PyTorch
Computer Science, Artificial Intelligence and Intelligent Systems
Library
Documentation, Uses, and more
blasr
lcc, mcc
1.0
Blasr is a read mapping program that maps reads to positions in a genome by clustering short exact matches between the read and the genome, and scoring clusters using alignment.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/blasr/blasr.html
Alignment, Sequencing, Genomics
Biology, Biological Sciences
Mapping
Documentation, Uses, and more
blast
lcc, mcc
1.0
BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/blast/blast.html
Bioinformatics, Sequence Alignment, Homology Search
Biological Sciences
Sequence Analysis Tool
Documentation, Uses, and more
blobtoolkit
mcc
1.0
Filtering raw genomic datasets is essential to avoid chimeric assemblies and to increase the validity of sequence-based biological inference. BlobToolKit extends the BlobTools1/Blobology2 approach to simplify interactive and reproducible filtering.
genomics, bioinformatics, data visualization, software tools
Computational Biology, Bioinformatics
Analysis Tool
Documentation, Uses, and more
blobtools
mcc
1.0
Blobtools is a modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/blobtools/blobtools.html
Genome Assembly, Data Visualization, Metagenomics
Biology, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
blobtools_v1.1.1
mcc
1.0
Documentation, Uses, and more
boltz
lcc
1.0
Documentation, Uses, and more
boost
lcc
N/A
Boost free peer-reviewed portable C++ source libraries
C++ Libraries, Programming Support, Efficiency Enhancement
Computer Science, Software Engineering, Systems & Development, Computer & Information Sciences
Development Tool
Documentation, Uses, and more
boost-devel
mcc
1.0
The Boost.MPL library is a general-purpose, high-level C++ template metaprogramming framework of compile-time algorithms, sequences and metafunctions. It provides a conceptual foundation and an extensive set of powerful and coherent tools that make doing explict metaprogramming in C++ as easy and enjoyable as possible within the current language.
c++, generic programming, system utilities, Libraries
Systems Programming, Computer Science
Library
Documentation, Uses, and more
bowtie
lcc, mcc
1.0
Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.
Description Source: https://bowtie-bio.sourceforge.net/manual.shtml
Bioinformatics, Genomics, DNA Sequencing, Sequence Alignment
Genetics, Biological Sciences
Alignment Tool
Documentation, Uses, and more
bowtie2
lcc, mcc
1.0
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning to relatively long (e.g. mammalian) genomes.
Description Source: https://github.com/BenLangmead/bowtie3
Alignment, Sequencing Reads, DNA Sequences, High-Throughput Sequencing, Bioinformatics, Genomics
Bioinformatics, Biological Sciences
Sequence Alignment
Documentation, Uses, and more
bpp
mcc
1.0
BPP is a Bayesian Markov chain Monte Carlo (MCMC) program for analyzing sequence alignments from multiple loci and multiple closely-related species under the multispecies coalescent (MSC) model. BPP takes into account episodic and continuous gene flow through its implementation of the multispecies coalescent with introgression (MSC-I) model for episodic events, and the multispecies coalescent with migration (MSC-M) model for continuous interactions.
phylogenetics, molecular evolution, comparative genomics
Evolutionary Biology, Life Sciences
Statistical Software
Documentation, Uses, and more
braker
lcc
1.0
BRAKER is a software tool for the automated gene prediction in eukaryotic genomes. It uses RNA-Seq data to improve the accuracy of gene models.
gene prediction, RNA-Seq, genomics, bioinformatics
Bioinformatics, Computational Biology
Bioinformatics Tool
Documentation, Uses, and more
braker3
mcc
1.0
BRAKER3 is a software tool for automated gene prediction in eukaryotic genomes, leveraging RNA-Seq data and protein homology.
Gene Prediction, Genome Annotation, Bioinformatics, RNA-Seq, Eukaryotic Genomes
Bioinformatics, Computational Biology
Bioinformatics Tool
Documentation, Uses, and more
breakdancer
lcc, mcc
1.0
a Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. BreakDancerMini focuses on detecting small indels (usually between 10bp and 100bp) using normally mapped read pairs.
genomics, bioinformatics, structural variants, next-generation sequencing
Genomic Analysis, Bioinformatics
Analysis Tool
Documentation, Uses, and more
bsbolt
lcc
1.0
a fast and scalable bisulfite sequencing analysis platform. BSBolt is an integrated analysis platform that offers support for bisulfite sequencing read simulation, alignment, methylation calling, data aggregation, and data imputation.
bisulfite sequencing, DNA methylation, read alignment, variant calling, epigenomics, bioinformatics
Epigenomics, Bioinformatics
Analysis software
Documentation, Uses, and more
build-essential
lcc, mcc
1.0
build-essential is a foundational Linux package that bundles the minimal compiler, linker, and build tools needed to turn source code into executable programs. It serves as a standard baseline for software development environments, ensuring that common C and C++ projects can be built reliably from source.
compiler toolchain, software compilation, development utilities
Software Engineering, Open Source Development
Package
Documentation, Uses, and more
busco
lcc, mcc
1.0
Benchmarking Universal Single-Copy Orthologs (BUSCO) is used for assessing genome assembly and annotation completeness.
Description Source: https://gitlab.com/ezlab/busco
Genomics, Genome Assembly, Gene Set, Transcriptome, Orthologs
Bioinformatics, Biological Sciences
Tools
Documentation, Uses, and more
bvalcalc
mcc
1.0
Documentation, Uses, and more
bwa
lcc, mcc
1.0
BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
Description Source: https://bio-bwa.sourceforge.net/
Sequence Alignment, Bioinformatics, Genomics, Next-Generation Sequencing (Ngs)
Biology, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
bwa-mem2
mcc
1.0
bwa-mem2 is a fast and accurate alignment tool for mapping DNA sequences against a reference genome, designed to handle large datasets efficiently.
bioinformatics, genomics, alignment, DNA sequencing
Bioinformatics, Genomics
Command-line tool
Documentation, Uses, and more
bwakit
mcc
1.0
bwakit is a bioinformatics tool designed for efficient and accurate processing of genomic data, particularly for handling large-scale sequencing data.
bioinformatics, genomics, sequencing, data processing
Bioinformatics, Genomics
Command-line tool
Documentation, Uses, and more
bwameth
mcc
1.0
Bwameth is a tool for fast and accurante alignment of BS-Seq reads.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bwameth/bwameth.html
DNA Methylation, Bisulfite Sequencing, Alignment, Bioinformatics
Genetics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
bx-python
mcc
1.0
bx-python is a Python library for bioinformatics that provides tools for manipulating and analyzing biological data, particularly in the context of genomic data.
bioinformatics, genomics, data analysis, Python
Genomics
Library
Documentation, Uses, and more
bzip2
ecc, lcc, mcc
1.0
bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
File Compression, Data Compression, Utility Software
General, Computer & Information Sciences
Compression Tool
Documentation, Uses, and more
bzip2-devel
lcc, mcc
1.0
Development files for the bzip2 compression library.
compression, decompression, file management, development
Computer Science, Software Engineering
Library
Documentation, Uses, and more
bzip2-libs
mcc
1.0
bzip2-libs is a library for data compression that uses the Burrows-Wheeler algorithm, providing high compression ratios and speed.
compression, data processing, libraries
Computer Science, Computer and Information Sciences
Library
Documentation, Uses, and more
c-blosc
lcc
N/A
c-blosc is a high-performance compressor optimized for binary data, designed to be used in conjunction with scientific computing applications.
compression, performance, binary data, scientific computing
Data Management, Data Compression
Library
Documentation, Uses, and more
ca-certificates
lcc, mcc
1.0
Documentation, Uses, and more
ca-certificates-mozilla
ecc
N/A
Documentation, Uses, and more
cactus
lcc
1.0
Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit. Description Source = https://github.com/ComparativeGenomicsToolkit/cactus?tab=readme-ov-file
Computational Software, Hpc Tools
Gravitational Physics, Physical Sciences
Simulation Software
Documentation, Uses, and more
cairo-devel
mcc
1.0
Cairo is a 2D graphics library that supports multiple output devices. It provides a vector-based drawing model and can produce output in various formats including PDF, PNG, and SVG.
Graphics, Rendering, 2D Graphics, Library
Software Engineering, Computer Science
Library
Documentation, Uses, and more
calder
mcc
1.0
Documentation, Uses, and more
canu
lcc, mcc
1.0
Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
Description Source: https://github.com/marbl/canu
Genome Assembly, Nanopore Sequencing, Long-Read Sequencing, Bioinformatics
Genomics, Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
canu-2.2
mcc
1.0
Canu is a software package for assembling genomes from single-molecule sequencing reads. It is designed for high-throughput sequencing technologies and provides tools for error correction, trimming, and assembly.
genome assembly, bioinformatics, high-throughput sequencing, single-molecule sequencing
Computational Biology, Bioinformatics
Assembly Software
Documentation, Uses, and more
ccl
ecc, lcc
N/A
CCL (Cpp Command Line Library) is a C++ library targeting Unix platform that makes it easy to define and parse command line arguments. It provides a simple and intuitive way to define and parse command-line arguments for C++ programs.
Command Line Interface, C++ Library
Documentation, Uses, and more
ccs/allmaps
lcc
N/A
Documentation, Uses, and more
ccs/amber
lcc
N/A
Amber MD application
Documentation, Uses, and more
ccs/anaconda
lcc
N/A
Documentation, Uses, and more
ccs/ansys/ansysedt
lcc
N/A
Documentation, Uses, and more
ccs/ansys/em
lcc
N/A
Documentation, Uses, and more
ccs/ansys/fluent
lcc
N/A
Documentation, Uses, and more
ccs/ansys/optislang
lcc
N/A
Documentation, Uses, and more
ccs/ansys/structures
lcc
N/A
Documentation, Uses, and more
ccs/arrayfire
lcc
N/A
Cell ranger tools .
Documentation, Uses, and more
ccs/automake
lcc
N/A
autoamke software.
Documentation, Uses, and more
ccs/bcl2fastq2
lcc
N/A
Cell ranger tools .
Documentation, Uses, and more
ccs/bonito
lcc
N/A
Documentation, Uses, and more
ccs/boost
lcc
N/A
Boost free peer-reviewed portable C++ source libraries
Documentation, Uses, and more
ccs/bpp
lcc
N/A
Documentation, Uses, and more
ccs/burai
lcc
N/A
Documentation, Uses, and more
ccs/cactus
lcc
N/A
Documentation, Uses, and more
ccs/canu
lcc
N/A
canu software.
Documentation, Uses, and more
ccs/cellranger
lcc
N/A
Cell ranger tools .
Documentation, Uses, and more
ccs/cellranger-arc
lcc
N/A
Cell ranger arc tools .
Documentation, Uses, and more
ccs/cellranger-atac
lcc
N/A
Cell ranger arc tools .
Documentation, Uses, and more
ccs/charmm
lcc
N/A
Documentation, Uses, and more
ccs/chemshell
lcc
N/A
canu software.
Documentation, Uses, and more
ccs/citcoms
lcc
N/A
Documentation, Uses, and more
ccs/comsol
lcc
N/A
Documentation, Uses, and more
ccs/conda/abyss
lcc
N/A
Documentation, Uses, and more
ccs/conda/admixture
lcc
N/A
Documentation, Uses, and more
ccs/conda/ambertools
lcc
N/A
Documentation, Uses, and more
ccs/conda/anvio
lcc
N/A
Documentation, Uses, and more
ccs/conda/ase
lcc
N/A
Documentation, Uses, and more
ccs/conda/augustus
lcc
N/A
Documentation, Uses, and more
ccs/conda/augustus-braker
lcc
N/A
Documentation, Uses, and more
ccs/conda/bcftools
lcc
N/A
Documentation, Uses, and more
ccs/conda/beagle-lib
lcc
N/A
Documentation, Uses, and more
ccs/conda/beast
lcc
N/A
Documentation, Uses, and more
ccs/conda/bedtools
lcc
N/A
Documentation, Uses, and more
ccs/conda/bioconductor-champ
lcc
N/A
Documentation, Uses, and more
ccs/conda/bioconductor-deseq2
lcc
N/A
Documentation, Uses, and more
ccs/conda/bioconductor-edger
lcc
N/A
Documentation, Uses, and more
ccs/conda/blast
lcc
N/A
Documentation, Uses, and more
ccs/conda/blat
lcc
N/A
Documentation, Uses, and more
ccs/conda/bowtie
lcc
N/A
Documentation, Uses, and more
ccs/conda/bowtie2
lcc
N/A
Documentation, Uses, and more
ccs/conda/braker
lcc
N/A
Documentation, Uses, and more
ccs/conda/busco
lcc
N/A
Documentation, Uses, and more
ccs/conda/bwa
lcc
N/A
Documentation, Uses, and more
ccs/conda/canu
lcc
N/A
Documentation, Uses, and more
ccs/conda/checkm-genome
lcc
N/A
Documentation, Uses, and more
ccs/conda/ciao
lcc
N/A
Documentation, Uses, and more
ccs/conda/circos
lcc
N/A
Documentation, Uses, and more
ccs/conda/colabfold
lcc
N/A
Documentation, Uses, and more
ccs/conda/cp2k
lcc
N/A
Documentation, Uses, and more
ccs/conda/crossmap
lcc
N/A
Documentation, Uses, and more
ccs/conda/cufflinks
lcc
N/A
Documentation, Uses, and more
ccs/conda/cutadapt
lcc
N/A
Documentation, Uses, and more
ccs/conda/deep-md-cpu
lcc
N/A
Documentation, Uses, and more
ccs/conda/deep-md-gpu
lcc
N/A
Documentation, Uses, and more
ccs/conda/dispy
lcc
N/A
Documentation, Uses, and more
ccs/conda/ensembl-vep
lcc
N/A
Documentation, Uses, and more
ccs/conda/fastqc
lcc
N/A
Documentation, Uses, and more
ccs/conda/fenics
lcc
N/A
Documentation, Uses, and more
ccs/conda/globus-cli
lcc
N/A
Documentation, Uses, and more
ccs/conda/graphviz
lcc
N/A
Documentation, Uses, and more
ccs/conda/hicup
lcc
N/A
Documentation, Uses, and more
ccs/conda/hisat2
lcc
N/A
Documentation, Uses, and more
ccs/conda/homer
lcc
N/A
Documentation, Uses, and more
ccs/conda/htseq
lcc
N/A
Documentation, Uses, and more
ccs/conda/hyphy
lcc
N/A
Documentation, Uses, and more
ccs/conda/intelpython3_full
lcc
N/A
Documentation, Uses, and more
ccs/conda/ipyrad
lcc
N/A
Documentation, Uses, and more
ccs/conda/jellyfish
lcc
N/A
Documentation, Uses, and more
ccs/conda/kallisto
lcc
N/A
Documentation, Uses, and more
ccs/conda/ligpargen
lcc
N/A
Documentation, Uses, and more
ccs/conda/macs2
lcc
N/A
Documentation, Uses, and more
ccs/conda/maker
lcc
N/A
Documentation, Uses, and more
ccs/conda/mashmap
lcc
N/A
Documentation, Uses, and more
ccs/conda/masurca
lcc
N/A
Documentation, Uses, and more
ccs/conda/matplotlib
lcc
N/A
Documentation, Uses, and more
ccs/conda/migrate-n
lcc
N/A
Documentation, Uses, and more
ccs/conda/mitoz
lcc
N/A
Documentation, Uses, and more
ccs/conda/mothur
lcc
N/A
Documentation, Uses, and more
ccs/conda/mpi4py
lcc
N/A
Documentation, Uses, and more
ccs/conda/mrbayes
lcc
N/A
Documentation, Uses, and more
ccs/conda/multiqc
lcc
N/A
Documentation, Uses, and more
ccs/conda/networkx
lcc
N/A
Documentation, Uses, and more
ccs/conda/nextflow
lcc
N/A
Documentation, Uses, and more
ccs/conda/notebook
lcc
N/A
Documentation, Uses, and more
ccs/conda/numba
lcc
N/A
Documentation, Uses, and more
ccs/conda/numpy
lcc
N/A
Documentation, Uses, and more
ccs/conda/ocelot
lcc
N/A
Documentation, Uses, and more
ccs/conda/ocelot_api
lcc
N/A
Documentation, Uses, and more
ccs/conda/openbabel
lcc
N/A
Documentation, Uses, and more
ccs/conda/openmm
lcc
N/A
Documentation, Uses, and more
ccs/conda/orthofinder
lcc
N/A
Documentation, Uses, and more
ccs/conda/paraview
lcc
N/A
Documentation, Uses, and more
ccs/conda/pathofact
lcc
N/A
Documentation, Uses, and more
ccs/conda/pdftotext
lcc
N/A
Documentation, Uses, and more
ccs/conda/perl
lcc
N/A
Documentation, Uses, and more
ccs/conda/phyluce
lcc
N/A
Documentation, Uses, and more
ccs/conda/picard
lcc
N/A
Documentation, Uses, and more
ccs/conda/pilon
lcc
N/A
Documentation, Uses, and more
ccs/conda/plink
lcc
N/A
Documentation, Uses, and more
ccs/conda/prank
lcc
N/A
Documentation, Uses, and more
ccs/conda/proovread
lcc
N/A
Documentation, Uses, and more
ccs/conda/psi4
lcc
N/A
Documentation, Uses, and more
ccs/conda/py2.7-samtools
lcc
N/A
Documentation, Uses, and more
ccs/conda/python
lcc
N/A
Documentation, Uses, and more
ccs/conda/r-base
lcc
N/A
Documentation, Uses, and more
ccs/conda/r-satscan
lcc
N/A
Documentation, Uses, and more
ccs/conda/racon
lcc
N/A
Documentation, Uses, and more
ccs/conda/raxml
lcc
N/A
Documentation, Uses, and more
ccs/conda/raxml-ng
lcc
N/A
Documentation, Uses, and more
ccs/conda/repeatmasker
lcc
N/A
Documentation, Uses, and more
ccs/conda/revbayes
lcc
N/A
Documentation, Uses, and more
ccs/conda/root
lcc
N/A
Documentation, Uses, and more
ccs/conda/rsem
lcc
N/A
Documentation, Uses, and more
ccs/conda/samtools
lcc
N/A
Documentation, Uses, and more
ccs/conda/scipy
lcc
N/A
Documentation, Uses, and more
ccs/conda/shtools
lcc
N/A
Documentation, Uses, and more
ccs/conda/sortmerna
lcc
N/A
Documentation, Uses, and more
ccs/conda/splicev
lcc
N/A
Documentation, Uses, and more
ccs/conda/sratoolkit
lcc
N/A
Documentation, Uses, and more
ccs/conda/stacks
lcc
N/A
Documentation, Uses, and more
ccs/conda/star
lcc
N/A
Documentation, Uses, and more
ccs/conda/stringtie
lcc
N/A
Documentation, Uses, and more
ccs/conda/structure
lcc
N/A
Documentation, Uses, and more
ccs/conda/subread
lcc
N/A
Documentation, Uses, and more
ccs/conda/telseq
lcc
N/A
Documentation, Uses, and more
ccs/conda/tk
lcc
N/A
Documentation, Uses, and more
ccs/conda/tophat
lcc
N/A
Documentation, Uses, and more
ccs/conda/trim-galore
lcc
N/A
Documentation, Uses, and more
ccs/conda/trimmomatic
lcc
N/A
Documentation, Uses, and more
ccs/conda/trinity
lcc
N/A
Documentation, Uses, and more
ccs/conda/trinotate
lcc
N/A
Documentation, Uses, and more
ccs/conda/ucsc-fatotwobit
lcc
N/A
Documentation, Uses, and more
ccs/conda/vcftools
lcc
N/A
Documentation, Uses, and more
ccs/conda/whatshap
lcc
N/A
Documentation, Uses, and more
ccs/container/gamess
lcc
N/A
GAMESS
Documentation, Uses, and more
ccs/container/hic-pro
lcc
N/A
Hic-Pro
Documentation, Uses, and more
ccs/container/matlab
lcc
N/A
MATLAB
Documentation, Uses, and more
ccs/container/opensees
lcc
N/A
Documentation, Uses, and more
ccs/container/p4vasp
lcc
N/A
p4vasp
Documentation, Uses, and more
ccs/container/qiime2
lcc
N/A
Documentation, Uses, and more
ccs/container/r/3.5.2
lcc
N/A
Documentation, Uses, and more
ccs/container/r/3.6.0
lcc
N/A
Documentation, Uses, and more
ccs/container/r/3.6.1
lcc
N/A
Documentation, Uses, and more
ccs/container/r/3.6.1-bioconductor
lcc
N/A
Documentation, Uses, and more
ccs/container/r/3.6.3
lcc
N/A
Documentation, Uses, and more
ccs/container/r/3.6.3-bioconductor
lcc
N/A
Documentation, Uses, and more
ccs/container/r/4.1.0
lcc
N/A
Documentation, Uses, and more
ccs/container/r/4.3.3
lcc
N/A
Documentation, Uses, and more
ccs/container/r/4.4.2
lcc
N/A
Documentation, Uses, and more
ccs/container/r/conda
lcc
N/A
Documentation, Uses, and more
ccs/container/r/rstan
lcc
N/A
Documentation, Uses, and more
ccs/container/sas
lcc
N/A
SAS
Documentation, Uses, and more
ccs/cortexassembler
lcc
N/A
assembler software.
Documentation, Uses, and more
ccs/cuda
lcc
N/A
Nvidia CUDA toolkit and samples
Documentation, Uses, and more
ccs/cudnn
lcc
N/A
Nvidia cudNN library
Documentation, Uses, and more
ccs/cufflinks
lcc
N/A
Cufflinks software.
Documentation, Uses, and more
ccs/dakota
lcc
N/A
Documentation, Uses, and more
ccs/diamond
lcc
N/A
diamond software.
Documentation, Uses, and more
ccs/dock6
lcc
N/A
Documentation, Uses, and more
ccs/eigen
lcc
N/A
eigen free peer-reviewed portable C++ source libraries
Documentation, Uses, and more
ccs/emboss
lcc
N/A
R is a language and environment for statistical computing and graphics (S-Plus like).
Documentation, Uses, and more
ccs/exonerate
lcc
N/A
Genomic software .
Documentation, Uses, and more
ccs/fftw
lcc
N/A
A Fast Fourier Transform library
Documentation, Uses, and more
ccs/finder
lcc
N/A
Finder software.
Documentation, Uses, and more
ccs/gamess
lcc
N/A
Documentation, Uses, and more
ccs/gatk
lcc
N/A
GATK tools .
Documentation, Uses, and more
ccs/gaussian/g16-a.03
lcc
N/A
Documentation, Uses, and more
ccs/git-lfs
lcc
N/A
git-lfs software.
Documentation, Uses, and more
ccs/gizmo
lcc
N/A
Documentation, Uses, and more
ccs/gmsh
lcc
N/A
Mesh software .
Documentation, Uses, and more
ccs/gromacs
lcc
N/A
Documentation, Uses, and more
ccs/gromacs-plumed2
lcc
N/A
Documentation, Uses, and more
ccs/gromacs-plumed2-gpu
lcc
N/A
Documentation, Uses, and more
ccs/gromacs/broadwell
lcc
N/A
Documentation, Uses, and more
ccs/gromacs/broadwell-gpu
lcc
N/A
Documentation, Uses, and more
ccs/gromacs/cascade
lcc
N/A
Documentation, Uses, and more
ccs/gromacs/cpu
lcc
N/A
Documentation, Uses, and more
ccs/gromacs/sandy-cpu
lcc
N/A
Documentation, Uses, and more
ccs/gromacs/skylake
lcc
N/A
Documentation, Uses, and more
ccs/gromacs/skylake-gpu
lcc
N/A
Documentation, Uses, and more
ccs/gsl
lcc
N/A
GNU Scientific Library (GSL)
Documentation, Uses, and more
ccs/hdf5
lcc
N/A
A general purpose library and file format for storing scientific data
Documentation, Uses, and more
ccs/hyphy-analysis
lcc
N/A
Documentation, Uses, and more
ccs/imagemagick
lcc
N/A
ImageMagick https://imagemagick.org/script/install-source.php
Documentation, Uses, and more
ccs/impi
lcc
N/A
Intel MPI Library (C/C++/Fortran for x86_64)
Documentation, Uses, and more
ccs/intel
lcc
N/A
Intel Compiler Family (C/C++/Fortran for x86_64)
Documentation, Uses, and more
ccs/java
lcc
N/A
Java jdk-11.0.2
Documentation, Uses, and more
ccs/jmodeltest
lcc
N/A
jmodeltest.
Documentation, Uses, and more
ccs/julia
lcc
N/A
Julia 1.1.0
Documentation, Uses, and more
ccs/lammps
lcc
N/A
Large-scale Atomic/Molecular Massively Parallel Simulator
Documentation, Uses, and more
ccs/latex
lcc
N/A
Documentation, Uses, and more
ccs/lcc-user
lcc
N/A
Documentation, Uses, and more
ccs/lcc-users
lcc
N/A
Documentation, Uses, and more
ccs/libtool
lcc
N/A
autoamke software.
Documentation, Uses, and more
ccs/lumerical
lcc
N/A
Lumerical software.
Documentation, Uses, and more
ccs/make
lcc
N/A
Make is an open-source, tool designed to build, test and package software.
Documentation, Uses, and more
ccs/maple
lcc
N/A
maple tool designed to package software.
Documentation, Uses, and more
ccs/mapsplice
lcc
N/A
Documentation, Uses, and more
ccs/matlab
lcc
N/A
Matlab tool designed to package software.
Documentation, Uses, and more
ccs/meryl
lcc
N/A
Documentation, Uses, and more
ccs/meshio
lcc
N/A
Documentation, Uses, and more
ccs/miniconda3
lcc
N/A
Documentation, Uses, and more
ccs/miniforge3
lcc
N/A
Documentation, Uses, and more
ccs/minimap2
lcc
N/A
minimap2 software.
Documentation, Uses, and more
ccs/mkl
lcc
N/A
Intel Compiler Family (C/C++/Fortran for x86_64)
Documentation, Uses, and more
ccs/molpro
lcc
N/A
Molpro software.
Documentation, Uses, and more
ccs/momap
lcc
N/A
momap software.
Documentation, Uses, and more
ccs/mono
lcc
N/A
mono software.
Documentation, Uses, and more
ccs/namd/2.13
lcc
N/A
Documentation, Uses, and more
ccs/netcdf-intel
lcc
N/A
Documentation, Uses, and more
ccs/nextflow
lcc
N/A
Documentation, Uses, and more
ccs/notung
lcc
N/A
Documentation, Uses, and more
ccs/nvidia/nvhpc
lcc
N/A
Documentation, Uses, and more
ccs/nwchem
lcc
N/A
Documentation, Uses, and more
ccs/orca
lcc
N/A
ab initio molecular dynamics package
Documentation, Uses, and more
ccs/paraview
lcc
N/A
Paraview tools .
Documentation, Uses, and more
ccs/patchelf
lcc
N/A
Documentation, Uses, and more
ccs/perl
lcc
N/A
Documentation, Uses, and more
ccs/pgi-cuda/18.10
lcc
N/A
Documentation, Uses, and more
ccs/pgi-cuda/2018
lcc
N/A
Documentation, Uses, and more
ccs/pgi-cuda/openmpi/2.1.2
lcc
N/A
Documentation, Uses, and more
ccs/pgi-cuda/pgi-llvm
lcc
N/A
Documentation, Uses, and more
ccs/pgi/18.10
lcc
N/A
Documentation, Uses, and more
ccs/pgi/2018
lcc
N/A
Documentation, Uses, and more
ccs/pgi/openmpi/2.1.2
lcc
N/A
Documentation, Uses, and more
ccs/phaser
lcc
N/A
Documentation, Uses, and more
ccs/plumed
lcc
N/A
Documentation, Uses, and more
ccs/pypy
lcc
N/A
Documentation, Uses, and more
ccs/quantumespresso
lcc
N/A
Documentation, Uses, and more
ccs/raxml-ng_v0.9.0
lcc
N/A
Documentation, Uses, and more
ccs/rosetta
lcc
N/A
rosetta software.
Documentation, Uses, and more
ccs/salome
lcc
N/A
salome software.
Documentation, Uses, and more
ccs/scflow
lcc
N/A
Documentation, Uses, and more
ccs/sda
lcc
N/A
Documentation, Uses, and more
ccs/shasta
lcc
N/A
shasta software.
Documentation, Uses, and more
ccs/singularity
lcc
N/A
Documentation, Uses, and more
ccs/singularity-devel
lcc
N/A
Documentation, Uses, and more
ccs/spaceranger
lcc
N/A
Cell ranger tools .
Documentation, Uses, and more
ccs/sratoolkit
lcc
N/A
sratoolkit software.
Documentation, Uses, and more
ccs/tassel
lcc
N/A
canu software.
Documentation, Uses, and more
ccs/totalview
lcc
N/A
Documentation, Uses, and more
ccs/ucx
lcc
N/A
Documentation, Uses, and more
ccs/vasp
lcc
N/A
Documentation, Uses, and more
ccs/vaspkit
lcc
N/A
vaspkit software.
Documentation, Uses, and more
ccs/vina
lcc
N/A
Autodock VINA software.
Documentation, Uses, and more
ccs/vmd
lcc
N/A
VMD https://www.ks.uiuc.edu/Research/vmd/
Documentation, Uses, and more
ccs/wrf
lcc
N/A
Documentation, Uses, and more
cd-hit
lcc, mcc
1.0
Cd-hit is a very widely used program for clustering and comparing protein or nucleotide sequences.
Sequence Analysis, Clustering, Bioinformatics
Bioinformatics, Biological Sciences
Bioinformatics Software
Documentation, Uses, and more
cd-hit-auxtools
lcc
1.0
cd-hit-auxtools is a set of auxiliary tools for the CD-HIT software, which is used for clustering and comparing biological sequences.
bioinformatics, sequence analysis, clustering
Bioinformatics, Biological Sciences
Command-line tool
Documentation, Uses, and more
cdbfasta
lcc
1.0
cdbfasta is a tool for converting sequence data in the CDB format to FASTA format, commonly used in bioinformatics for sequence analysis.
bioinformatics, sequence analysis, data conversion
Computational Biology, Genetics
Command-line tool
Documentation, Uses, and more
cdhit
lcc
1.0
CD-HIT is a program for clustering and comparing large sets of protein or nucleotide sequences. It is widely used in bioinformatics for reducing redundancy in sequence datasets.
bioinformatics, sequence clustering, data reduction
Computational Biology, Biological Sciences
Command-line tool
Documentation, Uses, and more
cdna_cupcake
lcc, mcc
1.0
Documentation, Uses, and more
cellbender
mcc
1.0
Cellbender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
Single-Cell RNA-Seq, Data Processing, Denoising, Batch Effects, Bioinformatics
Genetics, Biological Sciences
Python Library
Documentation, Uses, and more
cellranger
mcc
1.0
A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data.
Description Source: https://www.10xgenomics.com/support/software/cell-ranger/latest
Bioinformatics, Single-Cell RNA-Seq, Data Analysis
Biology, Biological Sciences
Documentation, Uses, and more
centrifuger
mcc
1.0
Documentation, Uses, and more
cgal
lcc
N/A
CGAL is an open source software project that provides easy access to efficient and reliable geometric algorithms in the form of a C++ library. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics.
Description Source: https://www.cgal.org/
Computational Geometry, Geometric Algorithms, Software Library
Computer Science, Computer & Information Sciences
Algorithm Library
Documentation, Uses, and more
cgmaptools
lcc
1.0
cgmaptools is a software package designed for the analysis of cytosine methylation data, particularly in the context of genomic studies.
bioinformatics, genomics, methylation analysis
Bioinformatics, Biochemistry and Molecular Biology
Analysis Tool
Documentation, Uses, and more
cgns
lcc
N/A
The CFD General Notation System (CGNS) provides a standard for recording and recovering computer data associated with the numerical solution of fluid dynamics equations. Description Source: https://github.com/conda-forge/cgns-feedstock/blob/main/recipe/meta.yaml
Computational Software
Fluid & Plasma Physics, Physical Sciences
File Format
Documentation, Uses, and more
charliecloud
lcc
N/A
Lightweight user-defined software stacks for high-performance computing
Containerization, Software Development, Research Tools
High-Performance Computing, Computer & Information Sciences
Tool
Documentation, Uses, and more
checkm-genome
lcc, mcc
1.0
Checkm-genome provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
Metagenomics, Microbial Ecology, Genome Quality Assessment
Environmental Biology, Biological Sciences
Genome Quality Assessment Tool
Documentation, Uses, and more
checkm2
mcc
1.0
CheckM2 is a software tool designed for assessing the completeness and contamination of microbial genomes, providing a comprehensive framework for quality control in metagenomic studies.
bioinformatics, genomics, metagenomics, quality control
Genomics, Microbiology
Command-line tool
Documentation, Uses, and more
checkv
mcc
1.0
CheckV is a tool designed to assess the quality of viral genomes assembled from metagenomic data, providing metrics on completeness and contamination.
bioinformatics, metagenomics, viral genomes, genome assembly
Bioinformatics, Biological Sciences
Command-line tool
Documentation, Uses, and more
chewbbaca
lcc
1.0
chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers.
Whole-Genome Analysis, Microbial Genotyping, Bacterial Typing, Phylogenetic Inference, Bioinformatics
Genomics, Biological Sciences
Tool
Documentation, Uses, and more
chopper
mcc
1.0
Chopper is Rust implementation of NanoFilt+NanoLyse, both originally written in Python.
Bioinformatics, Ngs Data Analysis, Sequence Trimming, High-Throughput Sequencing
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
clck
lcc
N/A
Documentation, Uses, and more
cli11
lcc
N/A
CLI11 is a command line parser for C++11 and beyond, designed to be easy to use and flexible.
C++, Command Line Interface, Parsing, Library
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
clinfo
lcc
1.0
clinfo is a command-line tool that provides detailed information about OpenCL platforms and devices available on a system.
OpenCL, GPU Computing, Performance Analysis
Computer Science, Computer and Information Sciences
Command Line Tool
Documentation, Uses, and more
clumpp
mcc
1.0
CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses. CLUMPP permutes the clusters output by independent runs of clustering programs such as structure, so that they match up as closely as possible.
population structure, clustering alignment, genetic analysis
Life Sciences, Bioinformatics
Analysis Tool
Documentation, Uses, and more
clumpp_linux64.1.1.2
mcc
1.0
CLUMPP (CLUMpifying Parallel Processes) is a software tool used for the analysis of population genetic data, particularly for clustering and assignment of individuals to populations based on genetic data.
Population Genetics, Clustering, Bioinformatics
Genetics, Bioinformatics
Analysis Tool
Documentation, Uses, and more
clust
mcc
1.0
Clust is a fully automated method for identification of clusters (groups) of genes that are consistently co-expressed (well-correlated) in one or more heterogeneous datasets from one or multiple species.
Clustering, Time Series Data, Pattern Identification
Other Computer & Information Sciences
Data Analysis Tool
Documentation, Uses, and more
cmake
ecc, lcc, mcc
1.0
CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
Build System, Cross-Platform, Software Development
Software Engineering, Systems & Development, Engineering & Technology
Developer Tools
Documentation, Uses, and more
cmake3
lcc
1.0
CMake is an open-source, cross-platform family of tools designed to build, test, and package software.
build system, cross-platform, open-source, software development
Software Development, Software Engineering
Build System
Documentation, Uses, and more
cmdstanr 0.5.2 and opencl
lcc
1.0
Documentation, Uses, and more
cogent
mcc
1.0
Cogent NGS Discovery Software (CogentDS) is bioinformatic software for user-friendly analysis of sequencing data generated with Takara Bio platforms. The Cogent NGS Analysis Pipeline (CogentAP) can be used to prepare files ready for import into CogentDS.
long-read sequencing, transcript reconstruction, isoform analysis
Life Sciences, Bioinformatics
Analysis Tool
Documentation, Uses, and more
colorama
lcc
1.0
Colorama is a Python library that makes it easy to print colored terminal text and styles on Windows, Linux, and macOS.
Python, Terminal, Text Formatting, Cross-platform
Computer Science, Software Engineering
Library
Documentation, Uses, and more
compiler
ecc, lcc
N/A
A compiler is a special program that processes statements written in a particular programming language and turns them into machine language or "code" that a computer's processor uses. It typically acts as a translator that converts high-level programming languages into machine language.
Compiler, Software Development, Programming
Software Engineering, Computer & Information Sciences
Compiler
Documentation, Uses, and more
compiler-intel-llvm
ecc
N/A
LLVM is a free and open source compiler infrastructure originally built for C and C++. Although its name initially stood for low-level virtual machine, LLVM is now a technology that deals with much more than just virtual machines. The name is no longer officially an initialism.
llvm, high-performance computing, intel optimization
High Performance Computing, Software Engineering
Compiler
Documentation, Uses, and more
compiler-rt
ecc, lcc
N/A
builtins - low-level target-specific hooks required by code generation and other runtime components sanitizer runtimes - AddressSanitizer, ThreadSanitizer, UndefinedBehaviorSanitizer, MemorySanitizer, LeakSanitizer, DataFlowSanitizer profile - library which is used to collect coverage information BlocksRuntime - target-independent implementation of Apple "Blocks" runtime interfaces Description Source: https://github.com/conda-forge/compiler-rt-feedstock/blob/main/recipe/meta.yaml
Runtime Library, Compiler Support, Low-Level Support, Language Features
Computer Science, Computer & Information Sciences
Library
Documentation, Uses, and more
compiler-rt32
lcc
N/A
The compiler-rt32 project is a runtime library that provides functionality for compilers in the 32-bit architecture. It includes various runtime components such as sanitizers, builtins, and support libraries for handling memory operations and error detection.
Compiler, Runtime Library, 32-Bit Architecture
Computer Science, Computer & Information Sciences
Runtime Library
Documentation, Uses, and more
compiler32
lcc
N/A
compiler32 is a lightweight and efficient compiler software designed for compiling source code into executable programs. It supports various programming languages and optimization techniques to enhance the performance of the compiled code.
Compiler, Software Development, Programming
Computer & Information Sciences
Development Tools
Documentation, Uses, and more
compleasm
mcc
1.0
Compleasm is a bioinformatics tool for assessing the completeness of genome assemblies using conserved single-copy orthologs. It provides a fast, lightweight alternative to BUSCO for evaluating genome quality, particularly in large-scale or high-throughput assembly workflows.
genome completeness, assembly evaluation, ortholog analysis
Computational genomics, Bioinformatics
Computational Biology Tool
Documentation, Uses, and more
conda-forge
ecc, lcc, mcc
1.0
conda-forge is a community effort and a GitHub organization which contains repositories of conda recipes and thus provides conda packages for a wide range of software. The built distributions are uploaded to anaconda.org/conda-forge and can be installed with conda.
package management,conda,open source,community
Scientific Computing Infrastructure, Data Science
Software Distribution Platform
Documentation, Uses, and more
conda-libmamba-solver
lcc, mcc
1.0
conda-libmamba-solver is a new solver for the conda package manager which uses the solver from the mamba project behind the scenes, while carefully implementing conda's functionality and expected behaviors on top. The library used by mamba to do the heavy-lifting is called libsolv.
package management, dependency resolution, conda, libmamba
Software Engineering, Computer Science
Dependency Solver
Documentation, Uses, and more
conmon
ecc
N/A
Conmon is a lightweight tool that provides a way to monitor and manage container processes. It is primarily used in conjunction with container runtimes to provide logging and lifecycle management for containers.
Containerization, Monitoring, Logging, Lightweight
Software Engineering, Other Computer and Information Sciences
Utility
Documentation, Uses, and more
coreutils
lcc
1.0
Coreutils is a package that provides the basic file, shell, and text manipulation utilities of the GNU operating system.
GNU, Command Line, Utilities, Open Source
Computer Science, Software Engineering
Command Line Tool
Documentation, Uses, and more
cortex_con
mcc
1.0
Documentation, Uses, and more
coseg
mcc
1.0
This program is derived from three C programs and several perl scripts written by Alkes Price as part of an analysis of Alu elements in the human genome. The program was first adapted for use with other repeat families and then extended to support consideration of three co-segregating mutations using Alkes statistical model. In 2008 with the help of Andy Siegel an alternative statistical model was developed and the codebase repackaged into the single source file.
co-segregation analysis, genomics, genetic variation, population genetics, comparative genomics, bioinformatics
Population Genetics, Bioinformatics
Bioinformatics analysis tool
Documentation, Uses, and more
coverm
mcc
1.0
Coverm is a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications.
Metagenomics, Bioinformatics, Genomics
Bioinformatics, Biological Sciences
Genomic Analysis Tool
Documentation, Uses, and more
cp2k
lcc, mcc
1.0
CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.
Description Source: https://www.cp2k.org/
Computational Chemistry, Quantum Mechanics, Molecular Dynamics
Physical Sciences
Molecular Simulation
Documentation, Uses, and more
cpanminus
lcc, mcc
1.0
cpanminus is a script to get, unpack, build and install modules from CPAN and does nothing else.\r
It's dependency free (can bootstrap itself), requires zero configuration, and stands alone. When running, it requires only 10MB of RAM.
Perl, CPAN, package management, dependency installation, command-line tool, developer tooling
Software Engineering, Computer Science
Package Manager
Documentation, Uses, and more
crackling
ecc, lcc, mcc
1.0
Documentation, Uses, and more
crest
mcc
1.0
Documentation, Uses, and more
csh
lcc
1.0
C shell (csh) is a Unix shell created by Bill Joy for the BSD Unix system. It is known for its C-like syntax and scripting capabilities.
Unix, Shell, Scripting, Command Line
Software Engineering, Other Computer and Information Sciences
Shell
Documentation, Uses, and more
cuda
lcc
1.0
The NVIDIA® CUDA® Toolkit provides a development environment for creating high performance GPU-accelerated applications. With the CUDA Toolkit, you can develop, optimize, and deploy your applications on GPU-accelerated embedded systems, desktop workstations, enterprise data centers, cloud-based platforms and HPC supercomputers.
Description Source: https://developer.nvidia.com/cuda-toolkit
Parallel Computing, Gpu Programming, High Performance Computing, Software Development
Computer Science, Computer & Information Sciences
Compiler
Documentation, Uses, and more
cuda-cudart-12
lcc
1.0
CUDA Runtime API for managing GPU resources and executing GPU kernels.
CUDA, GPU Computing, Parallel Computing
Computer Science, Computer and Information Sciences
Library
Documentation, Uses, and more
cuda-nvrtc-12
lcc
1.0
CUDA NVRTC (NVIDIA Runtime Compilation) is a library that allows for runtime compilation of CUDA C++ code, enabling dynamic generation of GPU kernels.
CUDA, GPU Programming, Runtime Compilation, NVIDIA
Computer Science, Software Engineering
Library
Documentation, Uses, and more
cudnn
lcc
1.0
The NVIDIA CUDA® Deep Neural Network (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. cuDNN provides highly tuned implementations for standard routines such as forward and backward convolution, attention, matmul, pooling, and normalization. \r
Description Source: https://docs.nvidia.com/cudnn/index.html
Deep Learning, Artificial Intelligence, Machine Learning, Gpu Acceleration, Neural Networks
Computer Science
Deep Learning Accelerator
Documentation, Uses, and more
cufflinks
mcc
1.0
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
Description Source: https://cole-trapnell-lab.github.io/cufflinks/
RNA-Seq, Transcriptomics, Bioinformatics
Biology, Biological Sciences
Tool
Documentation, Uses, and more
curl
ecc, lcc, mcc
1.0
libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
Networking, Data Transfer, Command-Line, Scripting
Computer Science, Computer & Information Sciences, Other Computer & Information Sciences
Networking Tool
Documentation, Uses, and more
cutadapt
lcc, mcc
1.0
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter single-end and paired-end reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Cutadapt can also demultiplex your reads.
Description Source: https://cutadapt.readthedocs.io/en/stable/
Bioinformatics, Ngs, Sequence Analysis, Genomics
Computational Biology, Biological Sciences
Sequence Analysis Tool
Documentation, Uses, and more
cython
lcc, mcc
1.0
Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself.
Description Source: https://cython.org/
Programming Language, C Extensions, Python, Cython
Computer Science, Computer & Information Sciences
Language Compiler
Documentation, Uses, and more
dal
lcc
N/A
DAL is a library for collision avoidance in robotics applications.
Robotics, Collision Avoidance
Engineering & Technology
Collision Avoidance Software
Documentation, Uses, and more
dartrverse
mcc
1.0
Documentation, Uses, and more
dask
lcc
1.0
Dask makes it easy to scale the Python libraries that you know and love like NumPy, pandas, and scikit-learn. It also allows you to Parallelize any Python code with Dask Futures, letting you scale any function and for loop, and giving you control and power in any situation.
Description Source: https://www.dask.org/
Parallel Computing, Scalable Computing, Analytics, Data Science
Data Analytics, Computer & Information Sciences
Library
Documentation, Uses, and more
datasets
ecc, lcc
1.0
Datasets is a lightweight library providing one-line dataloaders for many public datasets and one liners to download and pre-process any of the number of datasets major public datasets provided on the HuggingFace Datasets Hub. Datasets are ready to use in a dataloader for training/evaluating a ML model (Numpy/Pandas/PyTorch/TensorFlow/JAX). Datasets also provide an API for simple, fast, and reproducible data pre-processing for the above public datasets as well as your own local datasets in CSV/JSON/text. Description Source: https://github.com/conda-forge/datasets-feedstock/blob/main/recipe/meta.yaml
Data, Research, Analysis, Processing, Sharing
Documentation, Uses, and more
debugger
ecc, lcc
N/A
Intel® oneAPI Application Debugger (gdb-oneapi)
Debugging, Software Development
Engineering & Technology
Debugger
Documentation, Uses, and more
deepchem
lcc
1.0
DeepChem is a Python library for machine learning and deep learning on molecular and quantum datasets. It is built on top of PyTorch, and other popular ML frameworks. It is designed to make it easy to apply ML to new domains, and to build and benchmark new models. It is also designed to make it easy to use ML in production, by providing easy-to-use model export and deployment APIs.
deep learning, cheminformatics, drug discovery
Chemoinformatics, Drug Discovery
Library
Documentation, Uses, and more
deepchem-2.5.0-gpu
lcc
1.0
DeepChem is a Python library that aims to democratize the use of deep learning in drug discovery, bioinformatics, and cheminformatics.
Deep Learning, Bioinformatics, Chemoinformatics, Machine Learning
Bioinformatics, Drug Discovery
Library
Documentation, Uses, and more
deeppolisher
mcc
1.0
DeepPolisher is a transformer-based sequencing correction method similar to DeepConsensus. DeepPolisher is designed to identify errors in genome assemblies. DeepPolisher takes haplotype-specific reads aligned to phased assemblies and produces a VCF file containing potential errors in the assembly. Currently, DeepPolisher can take PacBio HiFi-based assemblies and read alignments to identify potential errors.
genome polishing, long-read sequencing, deep learning, neural networks, genome assembly, error correction, bioinformatics
Genome Assembly, Bioinformatics
Analysis software
Documentation, Uses, and more
deeptools
lcc, mcc
1.0
deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.
Description Source: https://deeptools.readthedocs.io/en/latest/
Bioinformatics, Hpc Tools, Computational Software
Biology, Biological Sciences
Analysis Tool
Documentation, Uses, and more
deepvariant
lcc, mcc
1.0
DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.
Variant Calling, Genetic Variants, Deep Learning, DNA Sequencing
Genomics, Biological Sciences
Variant Caller
Documentation, Uses, and more
default-jdk
lcc, mcc
1.0
The default Java Development Kit (JDK) for developing Java applications.
Java, Development, Programming, Software Engineering
Software Engineering
Development Kit
Documentation, Uses, and more
default-jre
mcc
1.0
The default Java Runtime Environment (JRE) for running Java applications.
Java, Runtime, JRE, Software Development
Software Engineering, Computer Science
Runtime Environment
Documentation, Uses, and more
delly
lcc
1.0
Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.
Structural Variant Discovery, Sv Detection, Genomics
Genomics, Biological Sciences
Tool
Documentation, Uses, and more
detonate
lcc
1.0
Documentation, Uses, and more
dev-utilities
ecc, lcc
N/A
Sample headers and CLI sample browser (oneapi-cli).
Development, Utilities
Computer & Information Sciences, Other Computer & Information Sciences
Tools
Documentation, Uses, and more
diamond
mcc
1.0
Diamond is sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.
Sequence Alignment, Ngs Analysis, Bioinformatics
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
diamond-linux64
mcc
1.0
Documentation, Uses, and more
diffdock
lcc
1.0
DiffDock is a software tool designed for molecular docking simulations, enabling the prediction of protein-ligand interactions with high accuracy and efficiency.
Molecular Docking, Bioinformatics, Computational Chemistry
Bioinformatics, Molecular Docking
Application
Documentation, Uses, and more
diffutils
ecc, lcc
1.0
GNU Diffutils is a package of several programs related to finding differences between files. Description Source: https://github.com/conda-forge/diffutils-feedstock/blob/main/recipe/meta.yaml
Text Comparison, File Difference, Text Analysis, Version Control
Software Engineering, Engineering & Technology
Text Processing
Documentation, Uses, and more
dimemas
lcc
N/A
Dimemas tool
Performance Prediction, Parallel Applications, Simulation, Large-Scale Systems
Computer Science, Engineering & Technology
Performance Prediction Tool
Documentation, Uses, and more
dm-tree
lcc
1.0
dm-tree is a python library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows to apply a function to each "leaf" preserving the overall structure.
Description Source: https://github.com/google-deepmind/tree
Python Library, Hierarchical Data, Tree Structures, Data Manipulation
Computer & Information Sciences
Library
Documentation, Uses, and more
dnf-plugins-core
lcc, mcc
1.0
Core plugins to use with DNF package manager.
DNF, RPM, Linux, package management, system administration, repository management, plugins
Software Engineering, Computer Science
Package Manager
Documentation, Uses, and more
dnnl
ecc, lcc
N/A
Performance library of basic building blocks for deep learning applications
Deep Learning, Neural Networks, Machine Learning, Performance Optimization
Artificial Intelligence & Intelligent Systems, Computer & Information Sciences
Deep Learning Library
Documentation, Uses, and more
dnnl-cpu-gomp
lcc
N/A
The dnnl-cpu-gomp is an open-source deep neural network library developed for CPU-based computations employing OpenMP (Open Multi-Processing) as a thread-processing technology.
Deep Learning, Neural Networks, Openmp, Cpu Computing
Machine Learning, Computer & Information Sciences
Computational Software
Documentation, Uses, and more
dnnl-cpu-iomp
lcc
N/A
dnnl-cpu-iomp is an optimization library for deep neural network computations on CPU using Intel OpenMP (iomp) for improved performance.
Deep Learning, Optimization, Cpu Acceleration
Computer & Information Sciences
Documentation, Uses, and more
dnnl-cpu-tbb
lcc
N/A
DNNL (Deep Neural Network Library) with TBB (Threading Building Blocks) support for optimized performance on CPU architectures.
Deep Learning, High-Performance Computing, Multi-threading, CPU Optimization
Artificial Intelligence, Artificial Intelligence and Intelligent Systems
Library
Documentation, Uses, and more
dorado
lcc, mcc
1.0
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
Description Source: https://github.com/nanoporetech/dorado
Performance Evaluation, Benchmarking, Hpc, Supercomputing
Biology, Engineering & Technology
Tool
Documentation, Uses, and more
dorodo
mcc
1.0
Documentation, Uses, and more
dos2unix
lcc
1.0
dos2unix converts text files with DOS or Mac line breaks to Unix line breaks and vice versa.
Description Source: https://dos2unix.sourceforge.io/#DOS2UNIX
Text Conversion, Line Endings, Command-Line Utility
Software Engineering, Computer & Information Sciences
Utility
Documentation, Uses, and more
double-conversion
lcc
N/A
Double-Conversion provides binary-decimal and decimal-binary routines for IEEE doubles. This library consists of efficient conversion routines that have been extracted from the V8 JavaScript engine.
Description Source: https://github.com/google/double-conversion
Conversion, Performance, Precision
Numerical Analysis, Computer & Information Sciences
Library
Documentation, Uses, and more
doxygen
lcc
N/A
Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
Documentation Generator, Software Development, Programming
Software Development, Software Engineering, Systems & Development
Tool
Documentation, Uses, and more
dpct
ecc, lcc
N/A
Migrate existing CUDA* code to SYCL code.
Cuda Programming, Gpu Computing, Parallel Programming
Computer Science, Computer & Information Sciences
Development Compiler
Documentation, Uses, and more
dpl
ecc, lcc
N/A
Intel(R) oneAPI DPC++ Library provides an alternative for C++ developers who create heterogeneous applications and solutions. Its APIs are based on familiar standards - C++ STL, Parallel STL (PSTL), Boost.Compute, and SYCL* - to maximize productivity and performance across CPUs, GPUs, and FPGAs.
Programming Language Analysis, Syntax Analysis, Language Structure Analysis
Documentation, Uses, and more
dplyr
lcc
1.0
dplyr is a grammar of data manipulation, providing a consistent set of verbs that help you solve the most common data manipulation challenges
Data Manipulation,R,Data Science,Statistics
Statistics, Data Analysis
Library
Documentation, Uses, and more
dram
mcc
1.0
Documentation, Uses, and more
drep
mcc
1.0
Drep is a python program for rapidly comparing large numbers of genomes.
Microbiome, Genome Analysis, Bioinformatics
Bioinformatics, Biological Sciences
Bioinformatics
Documentation, Uses, and more
dsuite
lcc, mcc
1.0
Dsuite provides a fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species.
Description Source: https://github.com/millanek/Dsuite
Python Library, Data Analysis, Data Visualization
Biostatistics, Statistics & Probability
Python Library
Documentation, Uses, and more
dvipng
lcc
1.0
This program makes PNG and/or GIF graphics from DVI files as obtained from TeX and its relatives.
LaTeX, TeX, DVI, PNG, document rendering, command-line utility, typesetting
Computational Publishing, Computer Science
Document processing utility
Documentation, Uses, and more
e2fsprogs
ecc
N/A
e2fsprogs is a set of utilities for creating, checking, and maintaining the ext2, ext3, and ext4 file systems in Linux.
Linux, File System, Utilities
Operating Systems, File Systems
Utility
Documentation, Uses, and more
e3nn
lcc
1.0
e3nn is a library for equivariant neural networks, designed to handle data with symmetry properties, particularly in the context of physical sciences and materials science.
Machine Learning, Neural Networks, Symmetry, Physics, Materials Science
Machine Learning, Neural Networks
Library
Documentation, Uses, and more
eagle_v2.4.1
mcc
1.0
The Eagle software estimates haplotype phase [1] either within a genotyped cohort or using a phased reference panel.
haplotype phasing, genotype data, population genetics, GWAS, imputation preprocessing, large-scale genomics
Population Genetics, Bioinformatics
Analysis software
Documentation, Uses, and more
eaglev
mcc
1.0
Documentation, Uses, and more
earlgrey
mcc
1.0
With the EarlGrey framework, you have access to enhanced synchronization features. EarlGrey automatically synchronizes with the UI, network requests, and various queues; but still allows you to manually implement customized timings, if needed.
General Tags transposable elements, repeat annotation, genome annotation, de novo TE discovery, eukaryotic genomes, bioinformatics pipeline
Evolutionary Genomics, Bioinformatics
Analysis software
Documentation, Uses, and more
easybuild
ecc, lcc
N/A
EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
Software Building, High-Performance Computing, Automation
Computer Science, Engineering & Technology
Build Automation
Documentation, Uses, and more
ecc/conda/astra-toolbox
ecc
N/A
ASTRA Toolbox 2.3.0 installed via Conda environment.
Documentation, Uses, and more
ecc/conda/python
ecc
N/A
Python 3.10 installed via Conda environment.
Documentation, Uses, and more
ecc/cuda
ecc
N/A
NVIDIA CUDA Toolkit 12.8.0 installed at /share/apps/cuda/12.8.0_570.86.10
Documentation, Uses, and more
ecc/miniconda3
ecc
N/A
Miniconda is a minimal installer for conda, a package manager and environment manager.
Documentation, Uses, and more
ecc/rclone
ecc
N/A
Rclone is a command-line tool for syncing files to and from cloud storage.
Documentation, Uses, and more
ecc/spack
ecc
N/A
Spack 0.23.1 is a flexible package manager for HPC environments.
Documentation, Uses, and more
ed
ecc
N/A
ed is a line-oriented text editor for Unix systems, designed for editing text files in a simple and efficient manner.
Text Editor, Unix, Command Line
Software Engineering, Other Computer and Information Sciences
Text Editing Tool
Documentation, Uses, and more
eggnog-mapper
mcc
1.0
Eggnog-mapper is a tool for fast functional annotation of novel sequences.
Functional Annotation, Orthology, Gene Function Prediction
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
eigen
lcc
N/A
Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
Description Source: https://eigen.tuxfamily.org/index.php?title=Main_Page
Linear Algebra, Numerical Computation, C++ Library
Applied Mathematics, Computer & Information Sciences
Linear Algebra Library
Documentation, Uses, and more
elfutils
ecc
N/A
elfutils is a collection of utilities and libraries to read, create and modify ELF binary files, find and handle DWARF debug data, symbols, thread state and stacktraces for processes and core files on GNU/Linux.
Description Source: https://sourceware.org/elfutils/
Binary Tool, Elf Files, Debugging, Programming
Software Engineering, Other Computer and Information Sciences
Utility
Documentation, Uses, and more
emboss
lcc
1.0
Emboss is 'The European Molecular Biology Open Software Suite'
Bioinformatics, Computational Biology, Sequence Analysis, Biological Data
Bioinformatics, Biological Sciences
Analysis Tool
Documentation, Uses, and more
ensembl-vep
lcc, mcc
1.0
VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
Description Source: https://useast.ensembl.org/info/docs/tools/vep/index.html
bioinformatics, genomics, variant analysis
Biology, Genetics
Command-line tool
Documentation, Uses, and more
ensembletr
mcc
1.0
EnsembleTR is a tool for ensemble Tandem Repeat (TR) calling. It takes one or more VCF files with TR genotypes for a panel of samples and outputs a consensus set of genotypes.
transcriptomics, RNA-seq, ensemble methods, gene expression, transcript reconstruction, bioinformatics
RNA Sequencing Analysis, Bioinformatics
Analysis software
Documentation, Uses, and more
entap
mcc
1.0
The Eukaryotic Non-Model Transcriptome Annotation Pipeline (EnTAP) is designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non-model eukaryotes.
transcriptome annotation, non-model organisms, functional annotation, ortholog identification, RNA-seq, bioinformatics pipeline
Genome Automation, Bioinformatics
Analysis software
Documentation, Uses, and more
epel-release
lcc, mcc
1.0
EPEL (Extra Packages for Enterprise Linux) is a repository of high-quality add-on packages for Enterprise Linux, including RHEL and CentOS.
Linux, Repository, Open Source, Enterprise
Software Engineering, Computer Science
Package Repository
Documentation, Uses, and more
exabayes
lcc
N/A
ExaBayes is a software package used for Bayesian inference of phylogenetic trees and parameters.
Bayesian Inference, Phylogenetics, Parallel Computing, Mcmc, Hpc
Ecology, Biological Sciences
Phylogenetic Software
Documentation, Uses, and more
excerpt
mcc
1.0
The extra-cellular RNA processing toolkit (exceRpt) was designed to handle the variable contamination and often poor quality data obtained from low input smallRNA-seq samples such as those obtained from extra-cellular preparations.
text processing, field extraction, command-line, Unix utilities, shell pipelines, data wrangling
Software Utilities, Computer Science
Command-line utility
Documentation, Uses, and more
exonerate
lcc
1.0
Exonerate is a generic tool for pairwise sequence comparison/alignment.
Sequence Alignment, Homology Search, Bioinformatics, Genomics
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
expat
ecc, lcc, mcc
1.0
Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)
Xml Parser, Library
Software Engineering, Computer & Information Sciences
Xml Parser
Documentation, Uses, and more
expat-devel
lcc, mcc
1.0
Expat is an XML parser library written in C. It is designed for high performance and is widely used in applications that require XML parsing.
XML, Parser, C, Library
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
extrae
lcc
N/A
Extrae tool
Performance Analysis, Trace Data, Parallel Applications, Distributed Applications
Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development, Engineering & Technology, Training, Infrastructure & Instrumentation
Tool
Documentation, Uses, and more
fast5
lcc
1.0
Documentation, Uses, and more
fastani
lcc, mcc
1.0
FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.
Description Source: https://github.com/ParBLiSS/FastANI
Bioinformatics, Genome Comparison, Bacterial Genomes
Biology, Biological Sciences
Genome Analysis Tool
Documentation, Uses, and more
fastp
lcc, mcc
1.0
Fastp is an ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging, etc).
Bioinformatics, Sequencing, Data Processing
Bioinformatics, Biological Sciences
Tool
Documentation, Uses, and more
fastqc
lcc
1.0
FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. Whereas Most sequencers will generate a QC report as part of their analysis pipeline, but this is usually only focused on identifying problems which were generated by the sequencer itself.
Description Source: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/1%20Introduction/1.1%20What%20is%20FastQC.html
Quality Control, High Throughput Sequencing, Sequence Analysis, Bioinformatics
Biology, Biological Sciences
Analysis Tool
Documentation, Uses, and more
fastsimcoal2
mcc
1.0
fastsimcoal2 is a software package designed for simulating and estimating demographic models in population genetics. It allows users to perform coalescent simulations and estimate parameters from genetic data.
Population Genetics, Coalescent Theory, Simulation, Demographic Modeling
Population Genetics
Simulation Software
Documentation, Uses, and more
faststructure
mcc
1.0
fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.
Population Genetics, Structural Biology, Genomics
Genetics, Biological Sciences
Inference Tool
Documentation, Uses, and more
fastx_toolkit
lcc, mcc
1.0
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
Description Source: http://hannonlab.cshl.edu/fastx_toolkit/
Bioinformatics, Short-Reads, Preprocessing
Biology, Biological Sciences
Pre-Processing Tool
Documentation, Uses, and more
feems
lcc, mcc
1.0
Documentation, Uses, and more
fenicsx
mcc
1.0
FEniCSx is a popular open-source computing platform for solving partial differential equations (PDEs) using finite element methods (FEM). It provides a high-level interface for defining and solving complex mathematical models.
Finite Element Method, Partial Differential Equations, Computational Science, Open Source
Applied Mathematics, Mathematics
Library
Documentation, Uses, and more
ffmpeg
mcc
1.0
FFmpeg is a collection of libraries and tools to process multimedia content such as audio, video, subtitles and related metadata. \r
Description Source: https://github.com/FFmpeg/FFmpeg
Media Processing, Multimedia, Video, Audio
Computer Science
Tool
Documentation, Uses, and more
fftw
lcc, mcc
1.0
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
Signal Processing, Data Compression, Partial Differential Equations
Applied Mathematics, Mathematics
Computational Software
Documentation, Uses, and more
fftw-devel
lcc, mcc
1.0
FFTW (Fastest Fourier Transform in the West) is a C library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
FFT, Fourier Transform, Numerical Computing, High Performance Computing
Numerical Methods, Applied Mathematics
Library
Documentation, Uses, and more
file
lcc, mcc
1.0
The file command is "a file type guesser", that is, a command-line tool that tells you in words what kind of data a file contains.
Description Source: https://www.darwinsys.com/file/
File Management, Command-Line Utility
Computer Science, Software Engineering
Command Line Tool
Documentation, Uses, and more
filtlong
mcc
1.0
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
Bioinformatics, Long Read Sequencing, Sequence Data Processing
Biological Sciences
Data Filtering Tool
Documentation, Uses, and more
finder
lcc
1.0
Documentation, Uses, and more
finder_v1.1.0
lcc
1.0
Documentation, Uses, and more
findutils
ecc, lcc
1.0
The GNU Find Utilities are the basic directory searching utilities of the GNU operating system. These programs are typically used in conjunction with other programs to provide modular and powerful directory search and file locating capabilities to other commands.
Unix, Linux, file searching, command-line tools, system utilities, shell scripting
Systems Programming, Computer Science
System utility software
Documentation, Uses, and more
finestructure
mcc
1.0
fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data. By using the output of ChromoPainter as a (nearly) sufficient summary statistic, it is able to perform model-based Bayesian clustering on large datasets, including full resequencing data, and can handle up to 1000s of individuals.
population genetics, haplotype analysis, genetic clustering, ancestry inference, ChromoPainter, genomics
Statistical Genetics, Bioinformatics
Analysis software
Documentation, Uses, and more
fixchr
mcc
1.0
Documentation, Uses, and more
flash
mcc
1.0
FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
Description Source: https://ccb.jhu.edu/software/FLASH/
Computational Software, Numerical Simulation, Fluid Dynamics, Electromagnetics, Structural Analysis
Physical Sciences
Computational Physics
Documentation, Uses, and more
flex
lcc
1.0
Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.
Lexical Analyzer, Text Processing, Pattern Matching, Scanner Generator
Software Engineering, Other Computer and Information Sciences
Compiler Tool
Documentation, Uses, and more
fltk
lcc
N/A
FLTK is a cross-platform C++ GUI toolkit for UNIX®/Linux® (X11), Microsoft® Windows®, and macOS®. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL® and its built-in GLUT emulation.
Description Source: https://www.fltk.org/
Gui Toolkit, Cross-Platform Development, C++ Library
Computer Science, Engineering & Technology
Development Tool
Documentation, Uses, and more
flye
lcc, mcc
1.0
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Genome Assembly, Long-Read Sequencing, Nanopore Sequencing
Genomics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
foss
lcc
N/A
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
Free Software, Open Source Software, Software Development
Other Computer & Information Sciences
Software Library
Documentation, Uses, and more
fpa
mcc
1.0
Documentation, Uses, and more
fragpipe
mcc
1.0
FragPipe is a software tool designed for the analysis of mass spectrometry data, particularly for proteomics applications. It provides a user-friendly interface and integrates various tools for data processing, including peptide identification and quantification.
Proteomics, Mass Spectrometry, Data Analysis, Bioinformatics
Biochemistry and Molecular Biology, Proteomics
Data Analysis Tool
Documentation, Uses, and more
freebayes
lcc, mcc
1.0
Freebayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
Genetic Variant Detector, Snp Detection, Indel Detection, Bayesian Algorithm
Bioinformatics, Biological Sciences
Tool
Documentation, Uses, and more
freeglut3-dev
lcc
1.0
freeglut is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library.
OpenGL, graphics programming, windowing, input handling, C/C++ development, visualization, FreeGLUT
Visual Computing, Graphics Programming
Library
Documentation, Uses, and more
freetype
lcc
N/A
FreeType is a freely available software library to render fonts.
Description Source: https://freetype.org/
Font Engine, Text Rendering, Typography
Software Engineering, Computer & Information Sciences
Font Engine
Documentation, Uses, and more
freetype-devel
mcc
1.0
A development package for the FreeType font rendering library, which is used to render fonts in various applications.
Font Rendering, Graphics, Library
Software Engineering, Computer Science
Library
Documentation, Uses, and more
fribidi-devel
mcc
1.0
Documentation, Uses, and more
fschat
lcc
1.0
Documentation, Uses, and more
funannotate
mcc
1.0
Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes.
Description Source: https://funannotate.readthedocs.io/en/latest/#
Genome Prediction, Genome Annotation, Fungi, Bioinformatics
Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
fuse-overlayfs
ecc
N/A
This project provides a convenient way to automatically perform a static build using a container. The result is a self-contained binary without dependencies, that can be copied across hosts.
FUSE,Overlay Filesystem,Userspace Filesystem,Linux
Systems Engineering, Computer Science
System utility software
Documentation, Uses, and more
galba
mcc
1.0
Documentation, Uses, and more
gangstr
mcc
1.0
GangSTR is a tool for genome-wide profiling tandem repeats from short reads.
Str, Genotyping, Short Tandem Repeats, Sequencing Data Analysis
Genomics, Biological Sciences
Genomic Analysis Tool
Documentation, Uses, and more
gapless
mcc
1.0
Documentation, Uses, and more
gapless-0.4
mcc
1.0
Documentation, Uses, and more
gatk
lcc, mcc
1.0
GATK (Genome Analysis Toolkit) is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery. The tools can be used individually or chained together into complete workflows.
Description Source: https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4
Variant Calling, Genotyping, Sequencing Analysis
Biology, Biological Sciences
Tool
Documentation, Uses, and more
gatk4
lcc, mcc
1.0
GATK (Genome Analysis Toolkit) is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discoverye.
Bioinformatics, Genomic Analysis, Variant Discovery, High-Throughput Sequencing
Biological Sciences
Genomic Analysis Tool
Documentation, Uses, and more
gawk
ecc
N/A
GaussView aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instruction, and helps in the interpretation of Gaussian output.
Description Source: https://gaussian.com/gaussview6/
Text Processing, Data Manipulation, Pattern Scanning
Chemistry, Computer & Information Sciences
Text Processing Tool
Documentation, Uses, and more
gbs-snp-crop
lcc
1.0
The GBS SNP Calling Reference Optional Pipeline (GBS-SNP-CROP) is executed via a sequence of seven Perl scripts that integrate custom parsing and filtering procedures with well-known, vetted bioinformatic tools, giving the user full access to all intermediate files.
genotyping-by-sequencing, SNP filtering, variant curation, linkage mapping, population genetics, plant genomics
Genetic Mapping, Bioinformatics
Analysis software
Documentation, Uses, and more
gcc
lcc, mcc
1.0
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
Compiler, Software Development, Programming
Computer Science
Development Tools
Documentation, Uses, and more
gcc-c++
lcc, mcc
1.0
GCC (GNU Compiler Collection) includes front ends for C and C++ among other languages. It is a widely used compiler for various programming languages, particularly in the open-source community.
Compiler, Open Source, C++, Programming
Computer Science, Software Engineering
Compiler
Documentation, Uses, and more
gcc-gfortran
lcc, mcc
1.0
GCC Fortran is the GNU Compiler Collection's Fortran compiler, which supports various versions of the Fortran programming language.
Compiler, Fortran, GCC, High-Performance Computing
Computer Science, Other Computer and Information Sciences
Compiler
Documentation, Uses, and more
gcc-runtime
ecc
N/A
The GCC Runtime Library is a part of the GCC compiler collection that provides runtime support for programs compiled with GCC. It includes various runtime libraries and support files necessary for programs compiled with GCC to execute correctly.
Compiler, Runtime, Library
Software Engineering, Systems & Development, Engineering & Technology
Runtime Library
Documentation, Uses, and more
gcc-toolset
lcc, mcc
1.0
The GCC Toolset is a collection of tools that provides a development environment for building and running applications using the GNU Compiler Collection (GCC). It includes various versions of GCC and related tools, enabling developers to compile and optimize their code efficiently.
Compiler, Development Tools, Open Source
Computer Science, Software Engineering
Development Tool
Documentation, Uses, and more
gcc_linux-64
lcc
1.0
The GNU Compiler Collection (GCC) is a compiler system produced by the GNU Project supporting various programming languages. The Linux 64-bit version is optimized for 64-bit Linux systems.
Compiler, Open Source, Programming, Development Tools
Computer Science
Compiler
Documentation, Uses, and more
gcccore
lcc
N/A
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
Compiler, Programming, Software Development
Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development
Core Component
Documentation, Uses, and more
gcta
lcc
1.0
GCTA (Genome-wide Complex Trait Analysis) is a software tool for estimating the proportion of phenotypic variance explained by all SNPs (Single Nucleotide Polymorphisms) in a genome-wide association study (GWAS). It is widely used in genetic epidemiology and quantitative genetics.
genetics, bioinformatics, GWAS, heritability, SNP analysis
Bioinformatics, Genetics
Analysis Tool
Documentation, Uses, and more
gdal
lcc, mcc
1.0
GDAL is a translator library for raster and vector geospatial data formats that is released under an MIT style Open Source License by the Open Source Geospatial Foundation.
Description Source: https://gdal.org/
Geospatial Data, Raster Data, Vector Data, Data Formats, Geospatial Analysis
Geographic Information Systems, Earth & Environmental Sciences, Engineering & Technology
Library
Documentation, Uses, and more
gdal-devel
mcc
1.0
GDAL (Geospatial Data Abstraction Library) is an open-source library for reading and writing raster and vector geospatial data formats. The 'gdal-devel' package includes development files for GDAL, enabling developers to build applications that utilize GDAL functionalities.
Geospatial, Data Processing, Open Source, Library
Environmental Science, Earth and Environmental Sciences
Library
Documentation, Uses, and more
gdbm
ecc, lcc
N/A
A library of database functions that use extensible hashing and works similar to the standard UNIX dbm functions. Description Source: https://github.com/conda-forge/gdbm-feedstock/blob/main/recipe/meta.yaml
Database Management, Key-Value Store, Persistent Storage, Api
Computer Science, Computer & Information Sciences
Library
Documentation, Uses, and more
gdbm-devel
mcc
1.0
gdbm-devel is a development library for the GNU database manager (GDBM), which provides a set of functions for managing a database using key-value pairs.
database, key-value store, data management, C library
Computer Science, Computer and Information Sciences
Library
Documentation, Uses, and more
geant4
lcc, mcc
1.0
Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
Software, Physics, Simulation, Particle Transport
Particle Physics, Physical Sciences
Toolkit
Documentation, Uses, and more
genmap
mcc
1.0
GenMap: Ultra-fast Computation of Genome Mappability.
Genetic Mapping, Linkage Analysis, Genetic Loci Mapping, Family-Based Studies
Biological Sciences
Genetic Mapping Software
Documentation, Uses, and more
genomad
mcc
1.0
Documentation, Uses, and more
genomescope2
mcc
1.0
Genomescope2: Reference-free profiling of polyploid genomes
Genome Analysis, Bioinformatics
Genomics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
genometools
mcc
1.0
GenomeTools is a versatile software package for the analysis and manipulation of genomic data. It provides a wide range of tools for tasks such as genome annotation, sequence analysis, and data visualization.
genomics, bioinformatics, sequence analysis, data visualization
Bioinformatics, Genomics
Open Source
Documentation, Uses, and more
geos-devel
mcc
1.0
Documentation, Uses, and more
getorganelle
lcc
1.0
Getorganelle is a fast and versatile toolkit for accurate de novo assembly of organelle genomes.
Bioinformatics, Genomics, Molecular Biology, Computational Biology
Genomics, Biological Sciences
Analysis Tool
Documentation, Uses, and more
gettext
ecc, lcc
N/A
GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation
Internationalization, Localization, Software Development
Software Engineering, Computer & Information Sciences
Localization Tool
Documentation, Uses, and more
gfacpp
mcc
1.0
Documentation, Uses, and more
gff3tool
lcc
1.0
Documentation, Uses, and more
gff3toolkit
lcc
1.0
Documentation, Uses, and more
ggplot2
lcc, mcc
1.0
ggplot2 is a data visualization package for the R programming language, based on the Grammar of Graphics. It provides a powerful and flexible way to create complex visualizations using a consistent and coherent approach.
Data Visualization, R, Statistical Graphics, Open Source
Statistics, Statistical Graphics
Library
Documentation, Uses, and more
ghostscript
lcc
1.0
Ghostscript is an interpreter for the PostScript® language and PDF files. It is available under either the GNU GPL Affero license or licensed for commercial use from Artifex Software, Inc. Ghostscript consists of a PostScript interpreter layer and a graphics library.
Description Source: https://ghostscript.com/
Document-Processing, File-Conversion, Print-Management
Computer Science, Computer & Information Sciences, Engineering & Technology
Software Development
Documentation, Uses, and more
gist-pipeline
lcc
1.0
Documentation, Uses, and more
gistpipeline
lcc
1.0
Documentation, Uses, and more
git
lcc, mcc
1.0
Git is a distributed version control system, widely used for tracking changes in source code during software development. It allows multiple developers to work collaboratively on a project, providing tools for managing versions, resolving conflicts, and maintaining a history of changes made to the codebase.
Version Control, Software Development, Source Code Management
Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development
Development Tools
Documentation, Uses, and more
gklib
mcc
1.0
A library of various helper routines and frameworks used by Karypis Lab software such as METIS.
Geometric Kernels, Computational Geometry, Algorithms
Applied Mathematics, Mathematics
Computational Software
Documentation, Uses, and more
glib
ecc
N/A
GLib is a general-purpose, portable utility library, which provides many useful data types, macros, type conversions, string utilities, file utilities, a mainloop abstraction, and so on. It is one of the base libraries of GTK+.
Description Source: https://docs.gtk.org/glib/
Utility Library, C Programming, Data Structures, Memory Management, Thread Support
Software Engineering, Computer & Information Sciences
Utility
Documentation, Uses, and more
glib2-devel
lcc
1.0
Development files for GLib, a low-level core library that forms the basis for projects such as GTK and GNOME.
C, Library, Development, Open Source
Computer Science, Software Engineering
Library
Documentation, Uses, and more
glibc
ecc
N/A
glibc, the GNU C Library, is an essential part of most systems running the Linux kernel. It provides the necessary functionality for programs written in the C programming language to interact with the operating system and hardware.
C Library, Operating System, System Programming
Computer & Information Sciences
Library
Documentation, Uses, and more
glibc-langpack-en
lcc, mcc
1.0
Documentation, Uses, and more
glibc-static
mcc
1.0
Documentation, Uses, and more
glimpse
mcc
1.0
Documentation, Uses, and more
glimpse-bio
mcc
1.0
Documentation, Uses, and more
glnexus
lcc, mcc
1.0
Glnexus: Scalable gVCF merging and joint variant calling for population sequencing projects.
Variant Calling, Genotyping, Haplotype-Aware, Bioinformatics
Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
glnexus-1.4.1
mcc
1.0
glnexus is a tool for genotyping and variant calling from genomic data, specifically designed to handle large-scale sequencing projects efficiently.
genomics, bioinformatics, variant calling, high-performance computing
Bioinformatics, Genomics
Command-line tool
Documentation, Uses, and more
glpk
mcc
1.0
The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
Description Source: https://www.gnu.org/software/glpk/
Linear Programming, Optimization, Open-Source
Applied Mathematics, Mathematics
Mathematical Optimization
Documentation, Uses, and more
glpk-devel
mcc
1.0
GLPK (GNU Linear Programming Kit) is a library for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems.
Linear Programming, Optimization, Mathematics, Software Development
Operations Research, Mathematics
Library
Documentation, Uses, and more
glproto
lcc
N/A
Documentation, Uses, and more
gmake
ecc
N/A
GNU Make is a tool that controls the generation of executables and other non-source files from a program's source files. It is widely used for managing build processes in software development.
Build Automation, Makefile, Open Source, GNU
Computer Science, Software Engineering
Build System
Documentation, Uses, and more
gmap
lcc
1.0
Gmap is a genomic mapping and alignment program for mRNA and EST sequences.
Bioinformatics, Computational Biology, Genomics, Transcriptomics, RNA-Seq
Genomics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
gmes_linux_64
lcc
1.0
Documentation, Uses, and more
gmp
ecc, lcc
N/A
GNU MP is a portable library written in C for arbitrary precision arithmetic on integers, rational numbers, and floating-point numbers. It aims to provide the fastest possible arithmetic for all applications that need higher precision than is directly supported by the basic C types.
Description Source: https://gmplib.org/manual/Introduction-to-GMP
Computational Software, Library, Mathematics, Software Development
Pure Mathematics, Mathematics
Library
Documentation, Uses, and more
gmsh
lcc, mcc
1.0
Gmsh is an open-source 3D finite element mesh generator with built-in CAD and post-processing capabilities, widely used for CFD, structural, and multiphysics simulations.
mesh generation, finite element analysis, CAD, post-processing
Engineering, Finite Element Analysis
Mesh Generator
Documentation, Uses, and more
gnu
lcc
N/A
GNU Compiler Family (C/C++/Fortran for x86_64)
Open Source, Development Tools, Utilities
Software Engineering, Computer Science
Development Tools
Documentation, Uses, and more
gnu-parallel
mcc
1.0
GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. The typical input is a list of files, a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU parallel can then split the input and pipe it into commands in parallel.
Description Source: https://www.gnu.org/software/parallel/
parallel computing, job scheduling, command-line tools, GNU, open-source
Computer Science
Command-line tool
Documentation, Uses, and more
gnu12
lcc
N/A
GNU Compiler Family (C/C++/Fortran for x86_64)
Documentation, Uses, and more
gnu14
ecc, lcc
N/A
GNU Compiler Family (C/C++/Fortran for x86_64)
Documentation, Uses, and more
gnu7
lcc
N/A
GNU Compiler Family (C/C++/Fortran for x86_64)
Documentation, Uses, and more
gnu8
lcc
N/A
GNU Compiler Family (C/C++/Fortran for x86_64)
Documentation, Uses, and more
gnupg
lcc
1.0
GnuPG (GNU Privacy Guard) is a free software replacement for Symantec's PGP cryptographic software suite. It allows users to encrypt and sign data and communications, providing a secure way to protect sensitive information.
Encryption, Security, Privacy, Open Source
Computer Security, Cryptography
Encryption Software
Documentation, Uses, and more
go
ecc
N/A
Go is expressive, concise, clean, and efficient. Its concurrency mechanisms make it easy to write programs that get the most out of multicore and networked machines, while its novel type system enables flexible and modular program construction. Go compiles quickly to machine code yet has the convenience of garbage collection and the power of run-time reflection. It's a fast, statically typed, compiled language that feels like a dynamically typed, interpreted language.
Description Source: https://go.dev/doc/
Programming Language, Open Source, Concurrency, Systems Programming
Software Engineering, Computer Science
Programming Language
Documentation, Uses, and more
go-bootstrap
ecc
N/A
go-bootstrap is a Go programming language template project that provides a starting point for building Go applications with a predefined project structure, configuration, and best practices.
Go, Template, Project Structure, Best Practices
Engineering & Technology
Template Project
Documentation, Uses, and more
go-md2man
ecc
N/A
A tool for converting Markdown files to man pages.
Markdown, Documentation, Man Pages
Software Engineering, Other Computer and Information Sciences
Command Line Tool
Documentation, Uses, and more
gocryptfs
ecc
N/A
gocryptfs is a user-space encryption tool for filesystems, designed to provide secure encryption of files and directories.
encryption, filesystems, security, data protection
Cryptography, Computer Science
Encryption Tool
Documentation, Uses, and more
gompi
lcc
N/A
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
Hpc, Parallel Computing, Mpi, Distributed Computing
Engineering & Technology
Documentation, Uses, and more
gperf
ecc
N/A
GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.
Description Source: https://www.gnu.org/software/gperf/
Perfect Hash Function, Hash Table, Optimization, Gnu
Computer Science, Computer & Information Sciences
Compiler/Generator
Documentation, Uses, and more
graphaligner
mcc
1.0
Documentation, Uses, and more
graphviz
mcc
1.0
Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.
Graph Visualization, Diagramming, Open Source Software
Graph Theory, Computer & Information Sciences
Data Visualization
Documentation, Uses, and more
grep
ecc
N/A
grep is a command-line utility for searching plain-text data sets for lines that match a regular expression.
Text Processing, Command Line Tool, Regular Expressions
Computer Science
Command Line Utility
Documentation, Uses, and more
grid
lcc
1.0
Documentation, Uses, and more
gridss
lcc
1.0
Gridss is a module software suite containing tools useful for the detection of genomic rearrangements.
Structural Variant Calling, DNA Sequencing, Genomic Rearrangements
Genetics, Biological Sciences
Tool
Documentation, Uses, and more
groff
mcc
1.0
groff (GNU roff) is a typesetting system that reads plain text input files that include formatting commands to produce output in PostScript, PDF, HTML, or DVI formats or for display to a terminal. Formatting commands can be low-level typesetting primitives, macros from a supplied package, or user-defined macros. All three approaches can be combined.
Description Source: https://www.gnu.org/software/groff/
Typesetting, Text Formatting, Unix Utilities
Computer Science, Computer & Information Sciences
Typesetting System
Documentation, Uses, and more
gromacs
lcc
1.0
GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world.
Molecular Dynamics, Simulation, High Performance Computing, Biomolecular Systems
Chemistry, Biological Sciences
Molecular Dynamics Software
Documentation, Uses, and more
gsalign
mcc
1.0
Documentation, Uses, and more
gsl
lcc, mcc
1.0
GNU Scientific Library (GSL)
Numerical Library, Mathematical Functions, C Programming, C++ Programming
Mathematics, Other Mathematics
Library
Documentation, Uses, and more
gsl-devel
lcc, mcc
1.0
The GNU Scientific Library (GSL) is a collection of routines for numerical computing in applied mathematics and science.
Numerical Analysis, Mathematics, Scientific Computing
Numerical Analysis, Mathematics
Library
Documentation, Uses, and more
gtdbtk
mcc
1.0
GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB.
bioinformatics, genomics, taxonomy, data analysis
Bioinformatics, Biological Sciences
Command-line tool
Documentation, Uses, and more
gtdbtk=2.4.1
mcc
1.0
GTDB-Tk is a toolkit for assigning taxonomic classifications to genomes based on the Genome Taxonomy Database (GTDB).
bioinformatics, genomics, taxonomy, data analysis
Bioinformatics, Biological Sciences
Command-line tool
Documentation, Uses, and more
gtf2csv
lcc, mcc
1.0
Documentation, Uses, and more
gth-1.7.3-linux_x86_64
lcc
1.0
Documentation, Uses, and more
gtools
lcc, mcc
1.0
gtools is a collection of R packages that provide various tools for data manipulation, analysis, and visualization, particularly in the context of genomic data.
R, Data Analysis, Genomics, Bioinformatics
Computational Biology, Genomics
Library
Documentation, Uses, and more
gubbins
lcc
1.0
Gubbins is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions.
Bacterial Recombination, Whole-Genome Sequencing, Population Genetics
Bioinformatics, Biological Sciences
Standalone
Documentation, Uses, and more
guidance
lcc
1.0
Documentation, Uses, and more
guppy
mcc
1.0
Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies' production basecalling algorithms and several bioinformatic post-processing features. It is run from the command line in Windows, Mac OS, and on multiple Linux platforms. Guppy is also integrated with our sequencing instrument software, MinKNOW, and a subset of Guppy features are available via the MinKNOW UI. A selection of configuration files allows basecalling of DNA and RNA libraries made with Oxford Nanopore Technologies’ current sequencing kits, in a range of flow cells.
Description Source: https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revax_14dec2018/guppy-software-overview
Bioinformatics, Sequencing, Nanopore Sequencing, Genomics, DNA Sequencing
Genomics, Biological Sciences
Basecaller
Documentation, Uses, and more
gzip
lcc, mcc
1.0
gzip is a single-file/stream lossless data compression utility, where the resulting compressed file generally has the suffix .gz. gzip also refers to the associated compressed data format used by the utility.
Description Source: https://www.gzip.org/
File Compression, Data Storage, Data Transfer
Computer Science, Engineering & Technology
Compression Tool
Documentation, Uses, and more
h5py
lcc
1.0
The h5py package is a Pythonic interface to the HDF5 binary data format. It lets you store huge amounts of numerical data, and easily manipulate that data from NumPy. For example, you can slice into multi-terabyte datasets stored on disk, as if they were real NumPy arrays. Thousands of datasets can be stored in a single file, categorized and tagged however you want.
Description Source: https://www.h5py.org/
Python Library, Data Storage, Numerical Data, Data Manipulation
Computational Science, Computer & Information Sciences
Library
Documentation, Uses, and more
harfbuzz-devel
mcc
1.0
HarfBuzz is an OpenType text shaping engine that provides advanced text rendering capabilities.
Text Rendering, Font Shaping, OpenType, Software Development
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
hdf5
lcc
N/A
HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
File Format, Data Management, Data Storage, Data Sharing, High-Performance Computing
Computational Science, Other Computer & Information Sciences
Library/Tool
Documentation, Uses, and more
help2man
lcc
N/A
help2man produces simple manual pages from the '--help' and '--version' output of other commands.
Documentation, Man Pages, Automation
Software Engineering, Systems & Development, Engineering & Technology
Utility
Documentation, Uses, and more
herro
lcc
1.0
Documentation, Uses, and more
hicpro
mcc
1.0
HiCPro is a software tool designed for the analysis of Hi-C data, which is used to study the three-dimensional architecture of genomes.
bioinformatics, genomics, data analysis
Computational Biology, Bioinformatics
Analysis Tool
Documentation, Uses, and more
hifiasm
mcc
1.0
Hifiasm is fast haplotype-resolved de novo assembler for PacBio HiFi reads.
Assembler, De Novo Assembly
Biological Sciences
Bioinformatics
Documentation, Uses, and more
hifiasm-0.25.0
mcc
1.0
Hifiasm is a high-performance assembler for long reads, designed to produce high-quality assemblies from high-throughput sequencing data.
genome assembly, bioinformatics, long-read sequencing
Computational Biology, Bioinformatics
Assembly Tool
Documentation, Uses, and more
hisat
lcc
1.0
HISAT is a fast and sensitive alignment program for mapping next-generation sequencing reads to a reference genome.
alignment, genomics, bioinformatics
Bioinformatics, Genomics
Command-line tool
Documentation, Uses, and more
hisat2
lcc, mcc
1.0
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. Based on an extension of BWT for graphs (Sirén et al. 2014), we designed and implemented a graph FM index (GFM), an original approach and its first implementation. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).
Description Source: https://daehwankimlab.github.io/hisat2/
Alignment, Ngs, Genomics, Transcriptomics
Biology, Biological Sciences
Alignment Tool
Documentation, Uses, and more
hmmer
lcc, mcc
1.0
HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
Description Source: http://hmmer.org/
Bioinformatics, Computational Biology, Proteomics, Sequence Analysis
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
hmmer2go
lcc
1.0
Documentation, Uses, and more
hocort
mcc
1.0
Documentation, Uses, and more
homer
mcc
1.0
HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.
Description Source: http://homer.ucsd.edu/homer/motif/
Bioinformatics, Next-Generation Sequencing, Motif Discovery, Transcription Factor Binding Sites
Genetics, Biological Sciences
Tool
Documentation, Uses, and more
htseq
lcc
1.0
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
Bioinformatics, RNA-Seq, High-Throughput Sequencing, Gene Expression, Sequence Data
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
htslib
lcc, mcc
1.0
HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang.
Description Source: https://github.com/samtools/htslib
Bioinformatics, Sequencing Data, File Format Processing, C Library
Genomics, Biological Sciences
Data Processing
Documentation, Uses, and more
humann
lcc, mcc
1.0
Humann is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads).
Metagenomics, Microbiome, Pathway Analysis, Bioinformatics
Biological Sciences
Analysis Tool
Documentation, Uses, and more
humann2
lcc
1.0
The HMP Unified Metabolic Analysis Network) is a method for efficiently and accurately determining the presence, absence, and abundance of metabolic pathways in a microbial community from metagenomic or metatranscriptomic sequencing data.
Genomics
Documentation, Uses, and more
humann=3.9
mcc
1.0
HUMAnN (The HMP Unified Metabolic Analysis Network) is a computational tool designed to profile the functional potential of microbial communities from metagenomic sequencing data.
metagenomics, bioinformatics, functional profiling, microbial ecology
Bioinformatics, Biochemistry and Molecular Biology
Command-line tool
Documentation, Uses, and more
hwloc
lcc
N/A
The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.
Machine Topology, Hardware Architecture, System Software
Computer Science, Computer & Information Sciences
Library
Documentation, Uses, and more
hyphy
lcc
1.0
Hyphy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.
Bioinformatics, Molecular Evolution, Phylogenetics, Epidemiology
Bioinformatics, Biological Sciences
Open-Source Software
Documentation, Uses, and more
hypo
mcc
1.0
HyPo--a Hybrid Polisher-- utilises short as well as long reads within a single run to polish a long reads assembly of small and large genomes.
Statistical Analysis, Hypothesis Testing, Data Analysis
Statistics & Probability
Scientific Software
Documentation, Uses, and more
hypre
lcc
N/A
Scalable algorithms for solving linear systems of equations
Preconditioners, Solvers, Linear Systems, Sparse Matrices
Applied Mathematics, Mathematics
Computational Software
Documentation, Uses, and more
icc
lcc
N/A
Intel C and C++ compilers
compiler, C++, performance, parallel computing
Software Engineering, Computer Science
Compiler
Documentation, Uses, and more
icc32
lcc
N/A
Documentation, Uses, and more
iccifort
lcc
N/A
Intel C, C++ & Fortran compilers
Compiler, High-Performance Computing, Optimization
Engineering & Technology
Programming Tool
Documentation, Uses, and more
idr
lcc, mcc
1.0
Documentation, Uses, and more
ifort
lcc
N/A
Intel Fortran compiler
Fortran, Compiler, High Performance Computing, Scientific Computing
Computer Science, Software Engineering
Compiler
Documentation, Uses, and more
ifort32
lcc
N/A
Intel® Fortran Compiler Classic for building optimized Intel® 64, and IA-32 CPUs
Documentation, Uses, and more
iimpi
lcc
N/A
Intel C/C++ and Fortran compilers, alongside Intel MPI.
Ion Mobility-Mass Spectrometry, Peak Integration, Data Analysis
Bioinformatics, Biological Sciences
Analytical Tool
Documentation, Uses, and more
imagemagick
mcc
1.0
ImageMagick is a free, open-source software suite, used for editing and manipulating digital images. It can be used to create, edit, compose, or convert bitmap images, and supports a wide range of file formats, including JPEG, PNG, GIF, TIFF, and PDF.
Image Processing, Graphics Editing, Conversion Tool
Image Processing, Computer & Information Sciences
Utility
Documentation, Uses, and more
imagemagick-devel
mcc
1.0
ImageMagick is a software suite to create, edit, and compose bitmap images. The 'devel' package includes development files necessary for compiling applications that use ImageMagick.
Image Processing, Graphics, Open Source
Applied Computer Science, Software Engineering
Library/Development Tools
Documentation, Uses, and more
imagemagick-libs
mcc
1.0
ImageMagick is a software suite to create, edit, and compose bitmap images. It can read, convert, and write images in a variety of formats.
Image Processing, Graphics, Open Source
Image Processing, Computer Science
Library
Documentation, Uses, and more
imb
lcc
N/A
Intel MPI Benchmarks (IMB)
Benchmarking, In-Memory Databases
Computer & Information Sciences
Tool
Documentation, Uses, and more
imkl
lcc
N/A
Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.
Software Library, Knowledge Graph, Artificial Intelligence, Data Science, Information Retrieval
Computer & Information Sciences, Artificial Intelligence & Intelligent Systems
Open-Source
Documentation, Uses, and more
impi
lcc
N/A
Intel MPI Library, compatible with MPICH ABI
Message Passing Library, Parallel Computing, Asynchronous Messaging
High-Performance Computing, Engineering & Technology
Communication Library
Documentation, Uses, and more
impi/2018.3.222
lcc
N/A
Intel MPI Library (C/C++/Fortran for x86_64)
Documentation, Uses, and more
impi/2019.3.199
lcc
N/A
Intel MPI Library (C/C++/Fortran for x86_64)
Documentation, Uses, and more
impi/2019.4.243
lcc
N/A
Intel MPI Library (C/C++/Fortran for x86_64)
Documentation, Uses, and more
impi/ccs/amber
lcc
N/A
Amber MD application
Documentation, Uses, and more
implicit-landuse
lcc
1.0
Documentation, Uses, and more
init_opencl
lcc
N/A
init_opencl is a software library that is used to initialize OpenCL platforms and create OpenCL contexts for parallel computing applications.
Software, Compiler, Library, Hpc
Computer & Information Sciences
Software Development
Documentation, Uses, and more
inotify-tools
lcc, mcc
1.0
A set of command-line programs for using inotify, a Linux kernel feature that monitors filesystem events.
Linux, File Monitoring, System Tools
Systems, Other Computer and Information Sciences
Command-line Tools
Documentation, Uses, and more
inputproto
lcc
N/A
A package that provides the headers used to compile Xlib clients.
Software Development, Headers, Xlib
Computer & Information Sciences
Library
Documentation, Uses, and more
inspector
lcc, mcc
1.0
Inspector is a software tool used for monitoring and analyzing various aspects of computer systems and networks to detect and prevent security breaches or performance issues.
Monitoring, Security, Network Analysis
Computer Science, Computer & Information Sciences
Security Software
Documentation, Uses, and more
intel
lcc
N/A
Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL).
Compiler, Optimization, Performance, Debugging
Computer and Information Sciences
Development Tools
Documentation, Uses, and more
intel-oneapi-compilers
lcc
N/A
Intel oneAPI Compilers provide a unified programming model for high-performance computing, enabling developers to optimize applications across various architectures including CPUs and GPUs.
compilers, high-performance computing, Intel, oneAPI, C++, Fortran
Computer Science, Software Engineering
Compiler
Documentation, Uses, and more
intel-oneapi-mpi
lcc
N/A
Intel oneAPI MPI is a high-performance message passing interface library designed to facilitate parallel programming in distributed computing environments.
MPI, Parallel Computing, High Performance Computing, Distributed Systems
Computer Science, Computer and Information Sciences
Library
Documentation, Uses, and more
intel_ipp_ia32
lcc
N/A
Intel Integrated Performance Primitives (IPP) for IA-32 architecture provides a set of highly optimized software functions for multimedia processing, data processing, and communications.
HPC, Performance Optimization, Multimedia Processing
Computer Science, Computer and Information Sciences
Library
Documentation, Uses, and more
intel_ipp_intel64
ecc, lcc
N/A
A library of multimedia and data processing optimized for Single Instruction, Multiple Data (SIMD) instructions.
Software Development, Performance Optimization, Data Processing, Signal Processing, Image Processing, Cryptography
Software Engineering, Computer & Information Sciences, Systems & Development
Commercial
Documentation, Uses, and more
intel_ippcp_ia32
lcc
N/A
Intel Integrated Performance Primitives - Cryptography (IPP-Crypto) is a library that provides highly optimized building blocks for a variety of encryption and decryption algorithms on Intel architecture processors. It aims to accelerate cryptographic operations to enhance performance in software applications.
Cryptographic Library, Performance Optimization, Intel Architecture
Computer & Information Sciences
Compiler/Library
Documentation, Uses, and more
intel_ippcp_intel64
ecc, lcc
N/A
Intel Integrated Performance Primitives Cryptography (IPP Cryptography) is a collection of highly optimized cryptographic functions and algorithms developed by Intel for high-performance computing applications. It provides a set of cryptographic functions optimized for Intel processors to enhance the security and performance of cryptographic operations in software.
Cryptography, High-Performance Computing, Intel Processors, Security
Computer & Information Sciences
Optimization Library
Documentation, Uses, and more
interproscan
lcc, mcc
1.0
Interproscan is the software package that allows sequences to be scanned against InterPro's member database signatures.
Bioinformatics, Proteomics, Sequence Analysis, Functional Annotation
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
interproscan-5.73-104.0
lcc, mcc
1.0
InterProScan is a tool for protein sequence analysis that integrates multiple databases and prediction methods to provide functional analysis of protein sequences.
bioinformatics, protein analysis, sequence analysis, functional annotation
Bioinformatics, Biological Sciences
Analysis Tool
Documentation, Uses, and more
iphop
mcc
1.0
Documentation, Uses, and more
ipykernel
lcc, mcc
1.0
IPython kernel for Jupyter, allowing interactive computing in Python.
Jupyter, Python, Interactive Computing, Data Science
Computer Science, Software Engineering
Kernel
Documentation, Uses, and more
ipyparallel
lcc, mcc
1.0
ipyparallel is a Python package for parallel computing that provides a simple interface for managing and executing parallel tasks across multiple processes and machines.
parallel computing, distributed computing, Python, IPython, Jupyter
Computer Science
Library
Documentation, Uses, and more
ipython
lcc, mcc
1.0
IPython is BSD-licensed, open-source software that is developed as a set of Subprojects under the ipython Github organization. These Subprojects are all part of the larger Project Jupyter umbrella. For further information about project governance, sponsorship and development, please see the Project page on Jupyter’s website.
Description Source: https://ipython.org/project.html
Command Shell, Interactive Computing, Data Visualization, Parallel Computing, Data Analysis
Computer Science, Computer & Information Sciences
Development Tools
Documentation, Uses, and more
iqtree
mcc
1.0
IQ-TREE is an efficient phylogenomic software by maximum likelihood.
Phylogenetics, Evolutionary Biology, Bioinformatics
Biochemistry and Molecular Biology, Phylogenetics
Standalone
Documentation, Uses, and more
iqtree-2.2.0_beta
mcc
1.0
IQ-TREE is a fast and effective software for phylogenomic analysis, providing maximum likelihood estimation of phylogenetic trees.
phylogenetics, bioinformatics, maximum likelihood, tree estimation
Computational Biology, Phylogenetics
Executable
Documentation, Uses, and more
isoseq
mcc
1.0
Iso-Seq is a method for full-length transcript sequencing that allows for the identification of isoforms and alternative splicing events in RNA sequencing data.
RNA-Seq, Transcriptomics, Bioinformatics
Bioinformatics, Molecular Biology
Command Line Tool
Documentation, Uses, and more
isoseq3
lcc, mcc
1.0
IsoSeq3 is a software tool for analyzing full-length transcript sequences generated by Pacific Biosciences (PacBio) sequencing technology. It focuses on the identification and characterization of isoforms in RNA sequencing data.
RNA-Seq, Transcriptomics, PacBio, Isoform Analysis
Molecular Biology, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
itac
lcc
N/A
The Intel® Trace Analyzer and Collector profiles and analyzes MPI applications to help focus your optimization efforts.
Description Source: https://www.intel.com/content/www/us/en/developer/tools/oneapi/trace-analyzer.html#gs.4oj2fp
Performance Analysis, Parallel Applications, Optimization
Computer & Information Sciences
Compiler
Documentation, Uses, and more
jags
lcc
1.0
JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.
Description Source: https://mcmc-jags.sourceforge.io/
Bayesian Statistics, Hierarchical Modeling, Mcmc Simulation
Statistics & Probability, Mathematics
Statistical Modeling
Documentation, Uses, and more
jasper
lcc
N/A
The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
Image Processing, Open-Source, Jpeg-2000
Computer Science, Computer & Information Sciences
Image Processing
Documentation, Uses, and more
java
lcc, mcc
1.0
Java is a programming language and computing platform first released by Sun Microsystems in 1995. It has evolved from humble beginnings to power a large share of today’s digital world, by providing the reliable platform upon which many services and applications are built. New, innovative products and digital services designed for the future continue to rely on Java, as well.
Description Source: https://www.java.com/en/download/help/whatis_java.html
Programming Language, Computing Platform
Software Engineering, Computer & Information Sciences
Compiler
Documentation, Uses, and more
java-jdk
mcc
1.0
The Java Development Kit (JDK) is a software development environment used for developing Java applications and applets.
Java, Development, Programming Language, Software Engineering
Software Engineering, Computer Science
Development Tools
Documentation, Uses, and more
jellyfish
lcc, mcc
1.0
Jellyfish is a fast and memory-efficient software for counting k-mers in DNA sequences, which are commonly used in genome analysis and sequence assembly. It provides algorithms for k-mer counting, storage, and querying to extract valuable insights from biological data.
K-Mer Counting, DNA Sequences, Sequence Analysis
Computational Biology, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
joblib
lcc
1.0
Joblib is a set of tools to provide lightweight pipelining in Python. It is particularly useful for saving and loading Python objects, especially large numpy arrays, efficiently.
Python, Parallel Computing, Serialization, Caching
Computer Science, Software Engineering
Library
Documentation, Uses, and more
jsoncpp
lcc
N/A
JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.
Description Source: https://github.com/open-source-parsers/jsoncpp
C++, Json, Library, Data Manipulation
Software Engineering, Computer & Information Sciences
Development Tools
Documentation, Uses, and more
juicebox_env
mcc
1.0
Documentation, Uses, and more
jupyter
mcc
1.0
JupyterLab is the latest web-based interactive development environment for notebooks, code, and data. Its flexible interface allows users to configure and arrange workflows in data science, scientific computing, computational journalism, and machine learning.
Data Science, Scientific Computing, Machine Learning
Data Analysis, Computer & Information Sciences
Web Application
Documentation, Uses, and more
jupyter_contrib_nbextensions
mcc
1.0
A collection of community-contributed extensions for Jupyter Notebook that enhance its functionality.
Jupyter, Notebook, Extensions, Python, Data Science
Computer Science, Data Science
Library
Documentation, Uses, and more
jupyterlab
ecc, lcc, mcc
1.0
JupyterLab is the latest web-based interactive development environment for notebooks, code, and data. Its flexible interface allows users to configure and arrange workflows in data science, scientific computing, computational journalism, and machine learning.
Interactive Computing, Data Visualization, Jupyter Notebooks, Web-Based Interface, Code Editing
Data Analysis, Computer & Information Sciences
Data Science Tool
Documentation, Uses, and more
kaiju
mcc
1.0
Kaiju is a tool for fast taxonomic classification of metagenomic sequencing reads using a protein reference database.
Bioinformatics, Computational Biology, Genomics, Sequencing Data
Biological Sciences
Sequence Analysis Tool
Documentation, Uses, and more
kallisto
mcc
1.0
Kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
RNA-Seq, Transcriptomics, Bioinformatics, Gene Expression Analysis, Computational Biology
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
kat
lcc, mcc
1.0
kat (K-mer Analysis Tool) is a software package designed for analyzing k-mer frequencies in DNA sequences, providing insights into genomic data.
bioinformatics, genomics, sequence analysis
Bioinformatics, Genomics
Analysis Tool
Documentation, Uses, and more
kbproto
lcc
N/A
The kbproto package provides the core XKB protocol and extension definitions for usage with X11 protocol libraries.
X11 Protocol, Keyboard Properties
Computer Science, Computer & Information Sciences
Protocol
Documentation, Uses, and more
keras
ecc
1.0
Keras is a deep learning API written in Python and capable of running on top of either JAX, TensorFlow, or PyTorch.
Description Source: https://keras.io/about/
Neural Networks, Deep Learning, Machine Learning
Artificial Intelligence & Intelligent Systems, Computer & Information Sciences
Library
Documentation, Uses, and more
kernel-devel
lcc
1.0
The kernel-devel package contains the development files for the Linux kernel, which are required for building kernel modules and for compiling software that depends on the kernel.
Linux, Kernel Development, System Programming, Open Source
Operating Systems, Kernel Development
Development Tools
Documentation, Uses, and more
kmc
mcc
1.0
Kmc is a tool for efficient k-mer counting and filtering of reads based on k-mer content.
Sequence Analysis, Genome Assembly, Metagenomics
Computational Biology, Biological Sciences
Tool
Documentation, Uses, and more
kneaddata
lcc, mcc
1.0
Kneaddata is a tool designed to perform quality control on metagenomic sequencing data.
Bioinformatics, Metagenomics, Data Quality Control
Biomolecular Sciences, Biological Sciences
Analysis Tool
Documentation, Uses, and more
kount
lcc
1.0
Documentation, Uses, and more
kraken-biom
lcc
1.0
Documentation, Uses, and more
kraken2
mcc
1.0
Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.
Description Source: https://github.com/DerrickWood/kraken2/wiki/About-Kraken-3
bioinformatics, sequence classification, metagenomics, taxonomy
Bioinformatics, Metagenomics
Command-line tool
Documentation, Uses, and more
kraken2-2.1.3
mcc
1.0
Kraken 2 is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences.
bioinformatics, sequence classification, metagenomics
Bioinformatics, Biological Sciences
Command-line tool
Documentation, Uses, and more
krakenuniq
mcc
1.0
KrakenUniq is a taxonomic sequence classifier that uses a unique k-mer approach to classify sequences from metagenomic data.
bioinformatics, metagenomics, sequence classification
Bioinformatics, Biological Sciences
Command-line tool
Documentation, Uses, and more
krona
mcc
1.0
Documentation, Uses, and more
lammps
lcc, mcc
1.0
LAMMPS is a classical molecular dynamics code with a focus on materials modeling. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.
Molecular Dynamics, Simulation, Computational Chemistry
Physical Chemistry, Chemical Sciences
Code/Package
Documentation, Uses, and more
lammps-mace
lcc
1.0
Documentation, Uses, and more
lammps-mace-mliap
lcc
1.0
Documentation, Uses, and more
lammpss-deepmd-kit-module-cpu
lcc
1.0
Documentation, Uses, and more
lammpss-deepmd-kit-module-gpu
lcc
1.0
Documentation, Uses, and more
lapack-devel
lcc
1.0
LAPACK (Linear Algebra PACKage) is a software library for numerical linear algebra. It provides routines for solving systems of linear equations, linear least squares problems, eigenvalue problems, and singular value decomposition.
Numerical Linear Algebra, High-Performance Computing, Scientific Computing
Applied Mathematics, Other Mathematics
Library
Documentation, Uses, and more
laser
mcc
1.0
Documentation, Uses, and more
lastz
lcc
1.0
LASTZ - pairwise DNA sequence aligner
Bioinformatics, DNA Sequencing, Alignment, Comparative Genomics
Genomics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
ldheatmap
lcc
1.0
Documentation, Uses, and more
lefse
mcc
1.0
LEfSe (Linear discriminant analysis Effect Size) is a tool for high-dimensional biomarker discovery and explanation. It is particularly useful in bioinformatics for analyzing microbiome data.
bioinformatics, microbiome, statistical analysis, biomarker discovery
Computational Biology, Biological Sciences
Analysis Tool
Documentation, Uses, and more
lefse=1.1.2
mcc
1.0
LEfSe (Linear discriminant analysis Effect Size) is a tool for high-dimensional biomarker discovery and explanation. It is particularly useful for identifying features that are statistically significant in biological data.
bioinformatics, statistical analysis, biomarker discovery
Biological Sciences, Biochemistry and Molecular Biology
Analysis Tool
Documentation, Uses, and more
less
mcc
1.0
less is a terminal pager program used to view the content of files one screen at a time. It allows backward and forward navigation through the file, making it easier to read large files in a command-line environment.
pager, command-line, file viewer, text processing
Software Engineering, Other Computer and Information Sciences
Utility
Documentation, Uses, and more
lftp
mcc
1.0
lftp is a file transfer program that allows sophisticated FTP, HTTP and other connections to other hosts. If site is specified then lftp will connect to that site otherwise a connection has to be established with the open command.
File Transfer
Networking, Computer Science
Command Line Tool
Documentation, Uses, and more
lhapdf
lcc
1.0
LHAPDF is a library for reading and interpolating parton distribution functions (PDFs) used in high-energy physics.
High-Energy Physics, Parton Distribution Functions, Computational Physics
High-Energy Physics, Particle and High-Energy Physics
Library
Documentation, Uses, and more
libarchive-devel
lcc, mcc
1.0
libarchive-devel is a development library for reading and writing streaming archives, including tar, cpio, zip, and ISO formats.
archive, compression, file management, development library
Computer Science, Software Engineering
Library
Documentation, Uses, and more
libbamtools-dev
lcc
1.0
libbamtools is a C++ library for reading, writing, and manipulating BAM files, which are binary versions of SAM files used in bioinformatics for storing large amounts of genomic data.
bioinformatics, genomics, data processing
Genomics, Genomic Data Processing
Library
Documentation, Uses, and more
libboost-all-dev
lcc
1.0
The Boost C++ Libraries are a set of libraries for the C++ programming language that provide support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, and regular expressions.
C++, Libraries, Boost, Development
Software Engineering, Computer Science
Library
Documentation, Uses, and more
libboost-iostreams-dev
lcc
1.0
Boost.Iostreams is a library that provides facilities for defining and using input and output streams in C++. It allows the creation of custom stream buffers and filters, enabling flexible data processing and manipulation.
C++, Boost, I/O Streams, Data Processing
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
libbsd
ecc, lcc
N/A
libbsd is a library that provides a collection of functions from the FreeBSD operating system for enhancing compatibility and portability across different Unix-like systems. It includes various system-related functions that are widely used in Unix programming to access system services and perform low-level operations.
Library, Bsd, Operating System
Software Engineering, Computer & Information Sciences
Library
Documentation, Uses, and more
libbz2-dev
lcc, mcc
1.0
libbz2-dev is a development library for the bzip2 compression algorithm, providing functions for compressing and decompressing data.
compression, decompression, data processing
Computer Science, Software Engineering
Library
Documentation, Uses, and more
libcairo2-dev
mcc
1.0
libcairo2-dev is a development package for the Cairo graphics library, which provides 2D graphics support for various output devices, including X Window System, Win32, and image buffers.
Graphics, Rendering, Development, Library
Software Development, Computer Science
Library
Documentation, Uses, and more
libcrypto++-dev
lcc, mcc
1.0
A free C++ library that provides a wide range of cryptographic algorithms and schemes.
Cryptography, C++, Security, Open Source
Applied Computer Science, Software Engineering
Library
Documentation, Uses, and more
libcublas-12
lcc
1.0
cuBLAS is a GPU-accelerated library for dense linear algebra that provides high-performance matrix-multiplication and other linear algebra operations.
CUDA, GPU Computing, Linear Algebra, High Performance Computing
Numerical Linear Algebra, Computer Science
Library
Documentation, Uses, and more
libcufft-12
lcc
1.0
libcufft-12 is a CUDA library for performing Fast Fourier Transforms (FFT) on NVIDIA GPUs, providing high-performance computing capabilities for scientific and engineering applications.
CUDA, FFT, High Performance Computing, NVIDIA, GPU Computing
Numerical Analysis, Signal Processing
Library
Documentation, Uses, and more
libcurl
mcc
1.0
libcurl is a free and easy-to-use client-side URL transfer library, supporting various protocols including HTTP, HTTPS, FTP, and more.
Networking, Data Transfer, Open Source, Library
Computer Science
Library
Documentation, Uses, and more
libcurl-devel
lcc, mcc
1.0
Development files for libcurl, a library for transferring data with URLs.
Networking, Data Transfer, Library, C/C++
Software Engineering, Computer Science
Library
Documentation, Uses, and more
libcurl4-gnutls-dev
lcc, mcc
1.0
Development files for libcurl with GnuTLS support.
Networking, Data Transfer, Library, Open Source
Software Engineering, Computer Science
Library
Documentation, Uses, and more
libcurl4-openssl-dev
lcc, mcc
1.0
libcurl4-openssl-dev is a development library that provides a way to transfer data with URLs. It supports various protocols including HTTP, HTTPS, FTP, and more, utilizing OpenSSL for secure connections.
Data Transfer, Networking, Open Source, Library
Computational Biology, Data Analysis
Library
Documentation, Uses, and more
libdb-dev
mcc
1.0
libdb-dev is a development library for Berkeley DB, a high-performance database library that provides developers with a variety of data storage and retrieval options.
database, storage, performance, ACID, key-value
Software Engineering, Computer Science
Library
Documentation, Uses, and more
libdbd-mysql-perl
mcc
1.0
libdbd-mysql-perl is a Perl module that provides a database driver for the MySQL database management system, allowing Perl applications to interact with MySQL databases using the DBI (Database Interface) framework.
Perl, Database, MySQL, DBI, Driver
Computer Science, Software Engineering
Library
Documentation, Uses, and more
libdbd-pg-perl
mcc
1.0
libdbd-pg-perl is a Perl module that provides a database driver for the PostgreSQL database management system, allowing Perl applications to interact with PostgreSQL databases using the DBI (Database Interface) framework.
Perl, Database, PostgreSQL, DBI, Driver
Database Management, Computer Science
Library
Documentation, Uses, and more
libdbd-sqlite3-perl
mcc
1.0
A Perl DBI driver for SQLite, allowing Perl applications to interact with SQLite databases.
Perl, Database, SQLite, DBI
Computer Science
Library
Documentation, Uses, and more
libdbi-perl
mcc
1.0
libdbi-perl is a Perl interface to the Database Independent Interface (DBI) library, allowing for database access in a portable manner.
Perl, Database, DBI, Data Access
Computer Science
Library
Documentation, Uses, and more
libedit
lcc
N/A
libedit is a library for reading and editing user input in a command-line interface. It provides tools for handling input editing, command history, and line parsing in a terminal environment.
Library, Command-Line, Line Editing, History, Open-Source
Software Engineering, Computer & Information Sciences
Tool
Documentation, Uses, and more
libeigen3-dev
mcc
1.0
Eigen is a C++ template library for linear algebra, including matrices, vectors, numerical solvers, and related algorithms.
C++, Linear Algebra, Matrix Operations, Numerical Methods
Numerical Analysis, Applied Mathematics
Library
Documentation, Uses, and more
libevent
lcc
N/A
Libevent is an event notification library for developing scalable network servers. The Libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, Libevent also support callbacks due to signals or regular timeouts.
Description Source: https://libevent.org/doc/
Event Notification, Callback Functions, Scalable, Efficient
Software Engineering, Computer & Information Sciences
Development
Documentation, Uses, and more
libexpat-dev
mcc
1.0
libexpat-dev is a library for parsing XML documents. It is a fast and efficient XML parser written in C, providing a simple API for developers to work with XML data.
XML, Parser, Library, C, Development
Software Engineering, Computer and Information Sciences
Library
Documentation, Uses, and more
libexpat1-dev
lcc
1.0
libexpat1-dev is a development package for the Expat XML parser library, which is a fast and efficient C library for parsing XML documents.
XML, Parser, C Library, Development
Software Engineering, Software Development
Library
Documentation, Uses, and more
libfabric
ecc, lcc
N/A
Development files for the libfabric library
Fabric Interfaces, High-Performance Computing, Communication Resources
Computer Science, Engineering & Technology
Communication Library
Documentation, Uses, and more
libffi
ecc, lcc
N/A
The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. FFI stands for Foreign Function Interface. A foreign function interface is the popular name for the interface that allows code written in one language to call code written in another language. The libffi library really only provides the lowest, machine dependent layer of a fully featured foreign function interface.
Description Source: https://github.com/libffi/libffi
Library, Portability, Calling Conventions
Software Engineering, Computer & Information Sciences
Development Tool
Documentation, Uses, and more
libffi-dev
mcc
1.0
libffi-dev is a foreign function interface library that provides a portable, high-level programming interface for calling functions in shared libraries and dynamically loaded modules.
C, Foreign Function Interface, Library, Cross-Platform
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
libffi-devel
lcc, mcc
1.0
libffi-devel is a development package for the Foreign Function Interface (FFI) library, which allows code written in one programming language to call code written in another.
FFI, Interoperability, Development, Libraries
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
libfontconfig1-dev
mcc
1.0
Development files for the Fontconfig library, which is used for font customization and management in various applications.
Font Management, Development, Library
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
libfreetype6-dev
mcc
1.0
Development files for the FreeType font rendering library.
font, rendering, graphics, library
Software Development, Computer Science
Library
Documentation, Uses, and more
libfribidi-dev
mcc
1.0
libfribidi-dev is a development library for the FreeBidi project, which provides bidirectional text support for applications. It is primarily used for rendering text in languages that are written from right to left, such as Arabic and Hebrew.
Text Processing, Bidirectional Text, Open Source
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
libfuse
ecc
N/A
libfuse is a library that allows the creation of fully functional file systems in userspace. It provides a simple interface for implementing file systems without the need for kernel-level code.
File System, Userspace, Linux, Development
Software Engineering, Computer Science
Library
Documentation, Uses, and more
libgd-dev
mcc
1.0
libgd-dev is a graphics library for the dynamic creation of images by programmers. It supports various image formats and provides functions for drawing shapes, text, and images.
Graphics, Image Processing, Library
Image Processing, Computer Science
Library
Documentation, Uses, and more
libgdbm-dev
mcc
1.0
libgdbm-dev is a development library for the GNU database manager (GDBM), which provides a simple interface for managing key-value pairs in a database format.
Database, Key-Value Store, Data Management
Computer Science
Library
Documentation, Uses, and more
libgl1-mesa-dev
mcc
1.0
libgl1-mesa-dev is a development package for the Mesa 3D Graphics Library, which provides an open-source implementation of OpenGL, Vulkan, and other graphics APIs.
Graphics, OpenGL, Development, 3D Rendering
Computer Science, Computer and Information Sciences
Library
Documentation, Uses, and more
libglvnd-devel
mcc
1.0
libglvnd-devel is a development library for the GL Vendor Neutral Dispatch library, which provides a mechanism for managing OpenGL implementations from different vendors.
OpenGL, Graphics, Development, Cross-platform
Software Development, Computer Science
Library
Documentation, Uses, and more
libgpg-error
ecc
N/A
libgpg is a library that provides an API for interacting with GnuPG (GNU Privacy Guard) for encryption, decryption, and key management tasks. It allows developers to integrate GnuPG functionality into their applications.
Error Handling, Library, Gnupg
Software Engineering, Computer & Information Sciences
Utility
Documentation, Uses, and more
libgsl-dev
lcc
1.0
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It provides a wide range of mathematical routines such as random number generators, special functions, and least-squares fitting.
Numerical Methods, Mathematics, C/C++, Scientific Computing
Mathematics, Applied Mathematics
Library
Documentation, Uses, and more
libharfbuzz-dev
mcc
1.0
HarfBuzz is an OpenType text shaping engine that provides advanced text layout capabilities.
Text Processing, Font Rendering, OpenType, Software Development
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
libhts-dev
lcc
1.0
libhts-dev is a library for handling HTS (Hierarchical Time Series) data, commonly used in bioinformatics for genomic data processing.
bioinformatics, genomics, data processing, HTS
Genomics, Bioinformatics
Library
Documentation, Uses, and more
libibumad
lcc
1.0
Documentation, Uses, and more
libibverbs
lcc, mcc
1.0
libibverbs is a library that provides a low-level API for accessing RDMA (Remote Direct Memory Access) capabilities in high-performance computing environments. It is primarily used for managing network connections and memory regions in systems that support RDMA.
RDMA, Networking, High-Performance Computing, InfiniBand, RoCE
Computer and Information Sciences, Other Computer and Information Sciences
Library
Documentation, Uses, and more
libibverbs-devel
lcc, mcc
1.0
libibverbs-devel is a development library for the InfiniBand and RDMA (Remote Direct Memory Access) networking stack, providing a low-level API for high-performance networking.
Networking, High-Performance Computing, InfiniBand, RDMA
Computer Science
Library
Documentation, Uses, and more
libibverbs-utils
lcc
1.0
libibverbs-utils provides utilities for managing and testing InfiniBand and RDMA (Remote Direct Memory Access) devices. It is part of the libibverbs library, which is used for high-performance networking in HPC environments.
HPC, Networking, RDMA, InfiniBand
Computer Science
Utility
Documentation, Uses, and more
libice
lcc
N/A
libice is a library that provides support for Inter-Client Exchange (ICE) in the X Window System, allowing X clients to securely exchange data through the X server.
Library, Inter-Client Exchange, X Window System
Computer & Information Sciences
Communication
Documentation, Uses, and more
libice-devel
lcc
1.0
Documentation, Uses, and more
libiconv
ecc, lcc
N/A
libiconv provides an iconv() implementation, for use on systems which don't have one, or whose implementation cannot convert from/to Unicode.
Description Source: https://www.gnu.org/software/libiconv/#TOCintroduction
Character Set Conversion, Text Data, Encoding
Other Computer & Information Sciences, Computer & Information Sciences
Conversion Tool
Documentation, Uses, and more
libint
lcc
N/A
libint is a library for the evaluation of molecular integrals of many-body operators over Gaussian functions.
Description Source: https://github.com/evaleev/libint?tab=readme-ov-file
Computational Chemistry, Molecular Integrals, Quantum Chemistry
Physical Chemistry, Chemical Sciences
Computational
Documentation, Uses, and more
libjpeg-dev
mcc
1.0
libjpeg-dev is a development library for handling JPEG image files. It provides functions for encoding and decoding JPEG images, making it essential for applications that require image processing.
Image Processing, JPEG, Library, Development
Image Processing, Computer Science
Library
Documentation, Uses, and more
libjpeg-turbo
lcc
N/A
libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, AVX2, Neon, AltiVec) to accelerate baseline JPEG compression and decompression on x86, x86-64, Arm, and PowerPC systems, as well as progressive JPEG compression on x86, x86-64, and Arm systems. On such systems, libjpeg-turbo is generally 2-6x as fast as libjpeg, all else being equal. On other types of systems, libjpeg-turbo can still outperform libjpeg by a significant amount, by virtue of its highly-optimized Huffman coding routines.
Description Source: https://libjpeg-turbo.org/
Image Compression, Jpeg Compression, Library, Open Source
Image Processing, Computer & Information Sciences
Compression Library
Documentation, Uses, and more
libjpeg-turbo-devel
mcc
1.0
libjpeg-turbo is a JPEG image codec that uses SIMD instructions to accelerate baseline JPEG compression and decompression.
image processing, JPEG, compression, decompression, performance
Software Engineering, Computer Science
Library
Documentation, Uses, and more
liblpsolve55-dev
lcc
1.0
liblpsolve55-dev is a library for solving linear programming (LP) and mixed integer programming (MIP) problems. It is designed to be used in various applications requiring optimization solutions.
Optimization, Linear Programming, Mixed Integer Programming, Mathematics
Mathematics, Applied Mathematics
Library
Documentation, Uses, and more
liblzma-dev
lcc, mcc
1.0
liblzma-dev is a development library for the LZMA compression algorithm, which is used for high compression ratios and is part of the XZ Utils package.
Compression, Data Management, Library
Computer Science
Library
Documentation, Uses, and more
libmd
ecc, lcc
N/A
libmd is a library for molecular dynamics simulations that allows for the integration of equations of motion for particles interacting with different potentials.
Molecular Dynamics, Simulation, Library
Physical Sciences
Computational
Documentation, Uses, and more
libmysql++-dev
lcc
1.0
libmysql++ is a C++ wrapper for the MySQL C API, providing a more convenient interface for database operations.
C++, Database, MySQL, Wrapper
Software Engineering, Computer Science
Library
Documentation, Uses, and more
libncurses-dev
mcc
1.0
libncurses-dev is a development library for creating text-based user interfaces in a terminal. It provides functions to control the display of text and manage user input, allowing developers to create interactive applications that run in a terminal environment.
C, Terminal, User Interface, Library
Computer Science, Software Engineering
Library
Documentation, Uses, and more
libncurses5-dev
lcc, mcc
1.0
Development files for ncurses, a library for controlling writing to the console.
C library, Terminal handling, Text user interface
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
libncursesw5-dev
lcc, mcc
1.0
Development files for the ncurses library, which provides functions to create text-based user interfaces in a terminal.
C, Library, User Interface, Terminal
Software Engineering, Computer and Information Sciences
Library
Documentation, Uses, and more
libnl3
lcc
1.0
libnl3 is a set of libraries providing APIs to work with the Linux kernel's netlink sockets, facilitating communication between the kernel and user-space applications.
Networking, Linux, Netlink, Socket Programming
Computer Science
Library
Documentation, Uses, and more
libnl3-cli
lcc
1.0
Documentation, Uses, and more
libnsl
mcc
1.0
Public client interface library for NIS(YP) Description Source: https://github.com/conda-forge/libnsl-feedstock/blob/main/recipe/meta.yaml
Network Services, Communication, Protocols
Computer Science, Computer & Information Sciences
System Software
Documentation, Uses, and more
libnvidia-gl
lcc
1.0
Documentation, Uses, and more
libogg
lcc
N/A
libogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs. As with all Xiph.org technology is it an open format free for anyone to use.
Description Source: https://www.xiph.org/ogg/
Library, Bitstream, Audio
Computer Science, Computer & Information Sciences
Data Format
Documentation, Uses, and more
libopencv-dev
lcc
1.0
libopencv-dev is a development package for OpenCV, a popular open-source computer vision and machine learning library that provides a comprehensive set of tools for image processing, computer vision, and machine learning tasks.
Computer Vision, Image Processing, Machine Learning, Open Source
Applied Computer Science, Computer Science
Library
Documentation, Uses, and more
libpciaccess
lcc
N/A
Generic PCI access library.
Library, Pci Bus Access, User-Space Drivers
Software Engineering, Computer & Information Sciences
Programming Library
Documentation, Uses, and more
libpng
lcc
N/A
libpng is the official PNG reference library. It supports almost all PNG features, is extensible, and has been extensively tested for over 28 years.
Description Source: http://www.libpng.org/pub/png/libpng.html
Image Processing, Graphics Library, Raster Images
Image Processing, Computer & Information Sciences
Data Handling
Documentation, Uses, and more
libpng-dev
mcc
1.0
libpng is a library for reading and writing PNG (Portable Network Graphics) image files.
Image Processing, Graphics, Library
Computer Science, Computer and Information Sciences
Library
Documentation, Uses, and more
libpng-devel
lcc, mcc
1.0
libpng-devel is a development package for the PNG (Portable Network Graphics) library, which is used for reading and writing PNG image files.
Image Processing, Graphics, Library
Computer Science, Other Computer and Information Sciences
Library
Documentation, Uses, and more
libpthread-stubs
lcc
N/A
Documentation, Uses, and more
libpython3-dev
mcc
1.0
The libpython3-dev package provides the development files for the Python 3 shared library, enabling the development of Python C extensions and embedding Python in C/C++ applications.
Python, Development, C Extensions
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
librdmacm
lcc, mcc
1.0
librdmacm is a library that provides a user-space API for the RDMA Communication Manager (RDMA CM), which is used for establishing connections and managing communication over RDMA-capable networks.
RDMA, Networking, High Performance Computing, User-space Library
Computer Science
Library
Documentation, Uses, and more
librdmacm-devel
lcc, mcc
1.0
librdmacm-devel is a development library for RDMA communication, providing an API for the RDMA Communication Manager (RDMA CM) to facilitate connection management and communication over RDMA-capable networks.
RDMA, Networking, High Performance Computing
Computer Science, Other Computer and Information Sciences
Library
Documentation, Uses, and more
librdmacm-utils
lcc
1.0
librdmacm-utils provides utilities for managing RDMA communication and resources, facilitating high-performance networking in computing environments.
RDMA, Networking, High-Performance Computing
Computer Science, Computer and Information Sciences
Utility
Documentation, Uses, and more
libreadline
lcc
N/A
The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
Command-Line Interface, Text Editing, Gnu Library, Interactive Programs
Software Engineering, Computer & Information Sciences
Utility
Documentation, Uses, and more
libseccomp
ecc
N/A
libseccomp is a library for implementing secure computing mode (seccomp) filters in Linux systems. It enables developers to apply fine-grained filtering on system calls, restricting the actions that processes can perform for improved system security.
Syscall Filtering, Linux Kernel, Security
Systems Security, Computer & Information Sciences
Development
Documentation, Uses, and more
libsigsegv
ecc, lcc
N/A
libsigsegv is a library for handling segmentation fault signals in Unix-like systems. It provides a mechanism for detecting, handling, and recovering from segment violation errors during program execution.
Library, Memory, Page Fault
Computer Science, Computer & Information Sciences
Utility
Documentation, Uses, and more
libsm
lcc
N/A
Libsm is a library that provides a set of common utilities for scientific computing in C++.
Library, Scientific Computing, C++
Other Natural Sciences
Library
Documentation, Uses, and more
libsm-devel
lcc
1.0
Documentation, Uses, and more
libsqlite3-dev
lcc
1.0
Development files for SQLite, a C library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine.
Database, SQL, C library, Embedded systems
Software Engineering, Computer Science
Library
Documentation, Uses, and more
libssl-dev
lcc, mcc
1.0
libssl-dev is a development package that provides the necessary headers and libraries for SSL and TLS implementations using OpenSSL, enabling secure communication over computer networks.
Security, Cryptography, Networking, OpenSSL
Software Engineering, Computer and Information Sciences
Library
Documentation, Uses, and more
libstdc++-static
mcc
1.0
libstdc++-static is the static version of the GNU Standard C++ Library, which provides a comprehensive set of C++ standard library functions and classes.
C++, Library, Static Linking, GNU
Software Engineering, Computer and Information Sciences
Library
Documentation, Uses, and more
libsuitesparse-dev
lcc
1.0
A collection of libraries for sparse matrix computations, including direct solvers and preconditioners.
Sparse matrices, Linear algebra, Numerical methods
Applied Mathematics, Other Mathematics
Library
Documentation, Uses, and more
libtheora
lcc
N/A
libtheora is a free and open-source software library for encoding and decoding video in the Theora format, which is a lossy video compression format.
video, codec, open-source, multimedia
Computer Science, Computer and Information Sciences
Library
Documentation, Uses, and more
libtiff
lcc
N/A
The LibTIFF software provides support for the Tag Image File Format (TIFF), a widely used format for storing image data.
Description Source: http://www.simplesystems.org/libtiff/
Image Processing, File Format, Library, Tiff, Image Storage
Computer Science, Computer & Information Sciences
Image Processing
Documentation, Uses, and more
libtiff-devel
mcc
1.0
libtiff-devel is a development library for reading and writing Tagged Image File Format (TIFF) images. It provides tools for handling TIFF files, including support for various compression schemes, color spaces, and metadata.
Image Processing, TIFF, Library, Development
Software Engineering, Computer Science
Library
Documentation, Uses, and more
libtiff5-dev
mcc
1.0
libtiff5-dev is a development library for reading and writing Tagged Image File Format (TIFF) files. It provides tools for handling TIFF images in various applications, particularly in the fields of imaging and graphics.
image processing, TIFF, graphics, development library
Software Engineering, Computer and Information Sciences
Library
Documentation, Uses, and more
libtool
ecc, lcc, mcc
1.0
GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
Library Management, Software Development, Compilation
Software Engineering, Engineering & Technology
Utility/Tool
Documentation, Uses, and more
libunwind
lcc
N/A
libunwind is a portable and efficient C API for determining the current call chain of ELF program threads of execution and for resuming execution at any point in that call chain. The API supports both local (same process) and remote (other process) operation.
Description Source: https://github.com/libunwind/libunwind
Debugging, Profiling, Runtime Instrumentation, Call Stack, C Programming
Software Engineering, Engineering & Technology
Development
Documentation, Uses, and more
libv8-dev
lcc, mcc
1.0
libv8-dev is a development package for the V8 JavaScript engine, which is used for executing JavaScript code in various applications, particularly in web browsers and server-side environments.
JavaScript, V8, Development, Engine
Software Engineering
Library
Documentation, Uses, and more
libx11
lcc
N/A
libx11 is the X11 protocol client library.
Description Source: https://gitlab.freedesktop.org/xorg/lib/libx11
X Window System, Client Library, Window System Interface, Graphics
Software Engineering, Computer & Information Sciences, Computer Science
Software Development
Documentation, Uses, and more
libx11-devel
lcc
1.0
Development files for the X11 client-side library.
X11, Development, Graphics, Libraries
Software Engineering, Computer and Information Sciences
Library
Documentation, Uses, and more
libxau
lcc
N/A
libXau is a library that provides authentication data for Xlib-based client programs.
Library, Authentication, Xlib
Computer & Information Sciences
Documentation, Uses, and more
libxc
lcc
N/A
libxc is a library of exchange-correlation and kinetic energy functionals for density-functional theory. The original aim was to provide a portable, well tested and reliable set of these functionals to be used by all the codes of the European Theoretical Spectroscopy Facility (ETSF), but the library has since grown to be used in several other types of codes as well; see below for a partial list.
Description Source: https://www.tddft.org/programs/libxc/
Quantum Mechanics, Computational Chemistry
Theoretical Chemistry, Chemical Sciences
Density Functional Theory
Documentation, Uses, and more
libxcb
lcc
N/A
The X protocol C-language Binding (libXCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.
Description Source: https://xcb.freedesktop.org/
X Window System, C Library, X Protocol
Computer Science, Computer & Information Sciences
Programming
Documentation, Uses, and more
libxcrypt
ecc
N/A
libxcrypt is a library for cryptographic hashing and password hashing, providing modern and secure algorithms for password storage and verification.
Cryptography, Security, Password Hashing, Libraries
Cryptography, Computer Science
Library
Documentation, Uses, and more
libxdmcp
lcc
N/A
libxdmcp is the X Display Manager Control Protocol library. It provides an API for the X Display Manager Control Protocol (XDMCP) for both the client and server side.
X11, Display Manager, Network Protocol
Software Engineering, Computer & Information Sciences
Networking
Documentation, Uses, and more
libxext
lcc
N/A
libXext is an extension library for the X Window System that provides additional functionality to the core Xlib library.
X Window System, Graphics, Library
Computer Science, Computer and Information Sciences
Library
Documentation, Uses, and more
libxext-devel
lcc
1.0
Development files for the X11 Extension library.
X11, Development, Libraries
Software Engineering, Computer and Information Sciences
Library
Documentation, Uses, and more
libxml2
ecc, lcc
N/A
Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
Xml, Html, Parsing, Validation, Manipulation
Software Engineering, Computer & Information Sciences
Parsing
Documentation, Uses, and more
libxml2-dev
lcc, mcc
1.0
libxml2-dev is a development package for the libxml2 library, which provides tools for parsing XML and HTML documents. It is widely used in various applications for its efficiency and flexibility in handling XML data.
XML, HTML, Parsing, Library, Development
Software Engineering, Software Development
Library
Documentation, Uses, and more
libxml2-devel
lcc, mcc
1.0
libxml2-devel is the development package for the libxml2 library, which provides tools for parsing XML and HTML documents. It includes the necessary headers and libraries for developing applications that utilize libxml2.
XML, HTML, Parsing, Development, Library
Software Engineering, Computer and Information Sciences
Library
Documentation, Uses, and more
libxrandr
lcc
N/A
libxrandr is a library that provides an interface to the X Resize and Rotate (RandR) extension of the X Window System, allowing applications to dynamically change the size, orientation, and reflection of the display.
X11, Graphics, Display Management
Software Engineering, Computer Science
Library
Documentation, Uses, and more
libxrender
lcc
N/A
libXrender is a library that provides an interface to the X Rendering Extension, which allows for the rendering of images and shapes in a more efficient manner than traditional X11 methods.
Graphics, Rendering, X11
Computer Science, Computer and Information Sciences
Library
Documentation, Uses, and more
libxslt1-dev
mcc
1.0
libxslt1-dev is a development package for the libxslt library, which is used for transforming XML documents into different formats using XSLT (Extensible Stylesheet Language Transformations).
XML, XSLT, Transformation, Library, Development
Software Engineering, Computer Science
Library
Documentation, Uses, and more
libxt
lcc
N/A
Libxt is a library offering extensions for automating compilation, dependency tracking, and execution of computational tasks within HPC environments.
Library, Hpc, Automation, Compilation, Dependency Tracking, Parallel Processing
Engineering & Technology
Library
Documentation, Uses, and more
libxt-devel
lcc, mcc
1.0
Documentation, Uses, and more
liftoff
mcc
1.0
Liftoff is an accurate GFF3/GTF lift over pipeline.
Build System, Ios Development, Macos Development, Software Development, Apple Platforms
Engineering & Technology
Build Automation
Documentation, Uses, and more
liftover
mcc
1.0
Liftover is a tool used to convert genomic coordinates between different assemblies or reference genomes.
genomics, bioinformatics, coordinate conversion, genome assembly
Bioinformatics, Genomics
Command-line tool
Documentation, Uses, and more
likwid
lcc
N/A
Toolsuite of command line applications for performance oriented programmers
Performance Analysis, Hpc, Performance Counter Profiling, Hardware Performance Counters
Performance Evaluation & Benchmarking, Engineering & Technology
Tool
Documentation, Uses, and more
lima
lcc, mcc
1.0
Lima is the standard tool to identify barcode and primer sequences in PacBio single-molecule sequencing data.
Single-Cell RNA-Seq, Data Analysis, Transcriptomics
Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
llama
ecc
1.0
Documentation, Uses, and more
llm-research
lcc
1.0
Documentation, Uses, and more
llvm
lcc
N/A
The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. Despite its name, LLVM has little to do with traditional virtual machines.
Description Source: https://llvm.org/
Compiler, Toolchain
Software Engineering, Computer & Information Sciences
Compiler
Documentation, Uses, and more
llvm5
lcc
N/A
LLVM Compiler Infrastructure
Compiler, Programming Language, Optimization, Toolchain
Software Engineering, Computer Science
Compiler Infrastructure
Documentation, Uses, and more
lmod
ecc, lcc, mcc
N/A
Lmod: An Environment Module System
Module Management, Software Environment, Environment Module System
Infrastructure & Instrumentation, Engineering & Technology
Utility
Documentation, Uses, and more
locale-gen
mcc
1.0
locale-gen is a command-line utility used in Unix-like operating systems to generate locale data based on the locale definitions specified in the system.
Localization, Internationalization, Command-line Tool
Software Engineering, Other Computer and Information Sciences
System Utility
Documentation, Uses, and more
locales
lcc, mcc
1.0
The locales package provides a way to manage and manipulate locale settings in programming environments, allowing for internationalization and localization of applications.
internationalization, localization, software development, programming
Software Engineering, Computer and Information Sciences
Library
Documentation, Uses, and more
longshot
mcc
1.0
Documentation, Uses, and more
longstitch
mcc
1.0
Documentation, Uses, and more
ltr_retriever
mcc
1.0
LTR_retriever is a software tool designed for the identification and retrieval of long terminal repeats (LTRs) in genomic sequences. It is particularly useful in the field of bioinformatics for studying transposable elements and their evolutionary dynamics.
bioinformatics, genomics, LTR retrotransposons, sequence analysis
Computational Biology, Genomics
Bioinformatics Tool
Documentation, Uses, and more
lua
ecc
N/A
Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.
Programming Language, Scripting Language, Embedded Systems
Software Engineering, Computer & Information Sciences
Programming Language
Documentation, Uses, and more
lua-luafilesystem
ecc
N/A
LuaFileSystem is a Lua library that provides a portable way to access the underlying filesystem. It allows users to perform operations such as file and directory manipulation, path manipulation, and more.
Lua, Filesystem, Library, Cross-platform
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
lua-luaposix
ecc
N/A
LuaPosix is a Lua binding for the POSIX API, providing access to operating system functionalities such as file manipulation, process control, and threading.
Lua, POSIX, Bindings, Operating System
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
lz4
ecc, lcc
N/A
LZ4 is lossless compression algorithm, providing compression speed > 500 MB/s per core (>0.15 Bytes/cycle). It features an extremely fast decoder, with speed in multiple GB/s per core (~1 Byte/cycle). A high compression derivative, called LZ4_HC, is available, trading customizable CPU time for compression ratio.
Description Source: https://lz4.org/
Compression, Data Compression, Lossless Compression
Computer Science, Computer & Information Sciences
Utility
Documentation, Uses, and more
lzma-dev
lcc
1.0
Documentation, Uses, and more
lzo
ecc
N/A
LZO offers pretty fast compression and extremely fast decompression. MiniLZO is a very lightweight subset of the LZO library. Description Source: https://github.com/conda-forge/lzo-feedstock/blob/main/recipe/meta.yaml
Data Compression, Algorithm, High-Speed
Computer Science, Computer & Information Sciences
Data Processing
Documentation, Uses, and more
m4
ecc, lcc
1.0
GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.
Macro Processor, Text Processing, Software Development, Build Process
Software Engineering, Computer & Information Sciences
Compiler
Documentation, Uses, and more
maaslin2
lcc
1.0
Maaslin2 is a tool for multivariate association analysis of microbiome data, allowing users to explore the relationships between microbial communities and various metadata factors.
bioinformatics, microbiome, statistics, data analysis
Bioinformatics, Microbial Ecology
Statistical Analysis Tool
Documentation, Uses, and more
macs
lcc
1.0
MACS (Model-based Analysis of ChIP-Seq) is a software tool designed for analyzing ChIP-Seq data to identify transcription factor binding sites.
ChIP-Seq, Bioinformatics, Genomics, Peak Calling
Bioinformatics, Genomics
Analysis Tool
Documentation, Uses, and more
macs2
lcc, mcc
1.0
MACS2 is Model-based Analysis of ChIP-Seq for identifying transcript factor binding sites.
Chip-Seq Analysis, Transcription Factor Binding Sites, Histone Modification, Bioinformatics
Biological Sciences
Command-Line Tool
Documentation, Uses, and more
mafft
lcc, mcc
1.0
MAFFT is a multiple alignment program for amino acid or nucleotide sequences.
Bioinformatics, Sequence Alignment, Phylogenetics
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
make
lcc, mcc
1.0
GNU Make is a tool which controls the generation of executables and other non-source files of a program from the program's source files.
Build Automation, Software Development, Programming
Computer Science, Engineering & Technology
Utility
Documentation, Uses, and more
maker
mcc
1.0
Maker is a portable and easily configurable genome annotation pipeline.
Genome Annotation, Bioinformatics
Genomics, Biological Sciences
Annotation Tool
Documentation, Uses, and more
mamba
mcc
1.0
Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux (ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda's commands.
Package Manager, Dependency Resolver, Environment Management
Software Engineering, Engineering & Technology
Package Manager
Documentation, Uses, and more
marty
lcc
1.0
Documentation, Uses, and more
mash-linux64
mcc
1.0
Mash is a tool for estimating the distance between genomic sequences using MinHash.
bioinformatics, genomics, sequence analysis
Bioinformatics, Genomics
Command-line tool
Documentation, Uses, and more
mashmap
mcc
1.0
Mashmap is a fast approximate aligner for long DNA sequences.
Mapping, Alignment, Genomics, Bioinformatics
Genomics, Biological Sciences
Bioinformatics
Documentation, Uses, and more
mashtree
lcc
1.0
Mashtree is a tool to create a tree using Mash distances.
Phylogenetic Trees, Genomic Similarity, Mash Distances
Genomics, Biological Sciences
Tool
Documentation, Uses, and more
masurca
mcc
1.0
The MaSuRCA (Maryland Super Read Cabog Assembler) genome assembly and analysis toolkit contains of MaSuRCA genome assembler, QuORUM error corrector for Illumina data, POLCA genome polishing software, Chromosome scaffolder, jellyfish mer counter, and MUMmer aligner.
Genome Assembly, Bioinformatics, Computational Biology
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
matplotlib
ecc, lcc, mcc
1.0
Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python. Matplotlib makes easy things easy and hard things possible.
Description Source: https://matplotlib.org/
Python Library, Data Visualization, Plotting Library
Computer Science, Computer & Information Sciences
Plotting & Graphing Tool
Documentation, Uses, and more
mcclintock
ecc, mcc
1.0
Documentation, Uses, and more
mcl
lcc
1.0
Mcl is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs
Clustering, Network Analysis, Graph Algorithms
Computational Biology, Computer & Information Sciences
Clustering Algorithm
Documentation, Uses, and more
mcscanx
mcc
1.0
MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa.
Gene Synteny, Genomic Analysis, Syntenic Relationships
Bioinformatics, Biological Sciences
Tool
Documentation, Uses, and more
mdanalysis
lcc
1.0
MDAnalysis is a Python library for the analysis of molecular dynamics simulations. It allows users to read, manipulate, and analyze trajectory data from various simulation software.
Molecular Dynamics, Simulation Analysis, Python, Scientific Computing
Molecular Dynamics, Biochemistry and Molecular Biology
Library
Documentation, Uses, and more
mdtraj
lcc
1.0
MDTraj is a Python library that allows users to analyze molecular dynamics trajectories. It provides tools to read, write, and manipulate trajectory data from various simulation packages.
Molecular Dynamics, Trajectory Analysis, Python, Bioinformatics
Molecular Dynamics, Biochemistry and Molecular Biology
Library
Documentation, Uses, and more
med
lcc
N/A
Documentation, Uses, and more
medaka
mcc
1.0
Medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data.
Bioinformatics, Ngs Data Analysis, Nanopore Sequencing, Consensus Sequence Calling
Bioinformatics, Biological Sciences
Ngs Data Analysis Tool
Documentation, Uses, and more
megahit
lcc, mcc
1.0
Megahit is a ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
Metagenome Assembly, Bioinformatics, Sequencing Data, Snp-Aware, Draft Assemblies
Bioinformatics, Biological Sciences
Assembly Software
Documentation, Uses, and more
megahit-1.2.9
mcc
1.0
MEGAHIT is a fast and memory-efficient tool for de novo assembly of large and complex metagenomic datasets.
metagenomics, assembly, bioinformatics
Bioinformatics, Biological Sciences
Command-line tool
Documentation, Uses, and more
megan
lcc
1.0
Megan is a computer program that allows optimized analysis of large metagenomic datasets. Metagenomics is the analysis of the genomic sequences from a usually uncultured environmental sample.
Metagenomics, Microbiome, Bioinformatics
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
megax
lcc
1.0
Documentation, Uses, and more
mesa
lcc
N/A
The Mesa project began as an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. Over the years the project has grown to implement more graphics APIs, including OpenGL ES, OpenCL, OpenMAX, VDPAU, VA-API, Vulkan and EGL.
Description Source: https://docs.mesa3d.org/index.html
Agent-Based Modeling, Complex Systems, Simulation, Computational Modeling
Other Computer & Information Sciences, Computer & Information Sciences
Framework
Documentation, Uses, and more
mesa-glu
lcc
N/A
mesa-gl is an open-source implementation of the OpenGL specification, a system for rendering interactive 3D graphics, and a widely used and versatile graphics library. mesa-glu is the OpenGL Utility Library (GLU) component of Mesa, providing useful functions for building OpenGL applications.
Graphics, 3D Graphics, Opengl, Graphics Library
Library
Documentation, Uses, and more
mesa-libgl
lcc
1.0
Mesa is an open-source implementation of OpenGL, Vulkan, and other graphics APIs. It provides a software renderer for OpenGL and is widely used in various graphics applications.
Graphics, Open Source, 3D Rendering, Cross-platform
Computer Science, Computer and Information Sciences
Library
Documentation, Uses, and more
meshlab
mcc
1.0
MeshLab is an open-source system for processing and editing 3D triangular meshes. It provides a set of tools for editing, cleaning, healing, inspecting, rendering, and converting meshes.
3D Modeling, Mesh Processing, Open Source
3D Modeling and Visualization, Computer Science
Desktop Application
Documentation, Uses, and more
meson
ecc, lcc
N/A
Meson is an open source build system meant to be both extremely fast, and, even more importantly, as user friendly as possible.
Description Source: https://mesonbuild.com/
Build System, Software Development, Automation
Computer Science, Computer & Information Sciences
Compiler
Documentation, Uses, and more
metabat2
mcc
1.0
MetaBAT 2 is a software tool designed for the binning of metagenomic assemblies, which helps in identifying and grouping sequences from environmental samples into their respective genomes.
metagenomics, binning, bioinformatics, sequence analysis
Bioinformatics, Metagenomics
Command-line tool
Documentation, Uses, and more
metaphlan
lcc, mcc
1.0
Metaphlan is computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level.
Metagenomics, Microbiome, Microbial Ecology, Bioinformatics
Environmental Biology, Biological Sciences
Tool
Documentation, Uses, and more
methods
lcc
1.0
Documentation, Uses, and more
methpipe
mcc
1.0
Documentation, Uses, and more
methyldackel
lcc, mcc
1.0
Methyldackel is a (mostly) universal methylation extractor for BS-seq experiments.
DNA Methylation, Bisulfite Sequencing, Epigenetics
Genetics, Biological Sciences
Data Analysis Tool
Documentation, Uses, and more
metis
lcc
N/A
Metis development files
Computational Software, Graph Partitioning, Mesh Partitioning, Hypergraph Partitioning
Computer Science, Computer & Information Sciences
Tool
Documentation, Uses, and more
mfem
lcc
N/A
Lightweight, general, scalable C++ library for finite element methods
Finite Element Method, C++ Library, Parallel Computing
Applied Mathematics, Engineering & Technology
Library
Documentation, Uses, and more
mhm2
mcc
1.0
MetaHipMer is a de novo metagenome short-read assembler. Version 2 (MHM2) is written entirely in UPC++ and runs efficiently on both single servers and on multinode supercomputers, where it can scale up to coassemble terabase-sized metagenomes.
Monte Carlo Simulation, Liquid Crystal Membranes, Bilayer Simulation
Physical Sciences
Computational Software
Documentation, Uses, and more
microbecensus
mcc
1.0
Documentation, Uses, and more
microbecensus-sourceapp
mcc
1.0
Documentation, Uses, and more
minigraph
lcc
1.0
Documentation, Uses, and more
minimap
mcc
1.0
Minimap is a versatile sequence alignment program that is designed for aligning long DNA or RNA sequences against a reference genome. It is particularly useful for applications in genomics and bioinformatics.
alignment, genomics, bioinformatics, sequence analysis
Bioinformatics, Sequence Alignment
Command-line tool
Documentation, Uses, and more
minimap2
lcc, mcc
1.0
Minimap2 is a versatile pairwise aligner for genomic and spliced nucleotide sequences.
Sequence Alignment, Bioinformatics, Genomics, Computational Biology
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
miranda
mcc
1.0
Documentation, Uses, and more
mirdeep
lcc
1.0
miRDeep is a computational tool for the identification of microRNAs from deep sequencing data.
bioinformatics, microRNA, deep sequencing, RNA analysis
Molecular Biology, Biochemistry and Molecular Biology
Analysis Tool
Documentation, Uses, and more
mirdeep2
lcc, mcc
1.0
miRDeep2 discovers active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...).
Bioinformatics, Computational Biology
Genetics, Biological Sciences
Tool
Documentation, Uses, and more
mitobim
lcc
1.0
mitobim is a software tool designed for the assembly and analysis of mitochondrial genomes from next-generation sequencing data.
bioinformatics, genomics, mitochondrial DNA, next-generation sequencing
Bioinformatics, Mitochondrial Genomics
Open-source
Documentation, Uses, and more
mitofinder
lcc
1.0
Mitofinder is a pipeline to assemble mitochondrial genomes and annotate mitochondrial genes from trimmed read sequencing data.
Bioinformatics, Genomics, Mitochondrial Genomes, Next-Generation Sequencing, Annotation
Genomics, Biological Sciences
Annotation Tool
Documentation, Uses, and more
mitohifi
lcc, mcc
1.0
Documentation, Uses, and more
mitoz
lcc
1.0
Mitoz is a software tool designed for the analysis of mitochondrial DNA sequences, particularly focusing on the identification and quantification of mitochondrial variants in genomic data.
bioinformatics, genomics, mitochondrial analysis
Bioinformatics, Genomics
Analysis Tool
Documentation, Uses, and more
mkl
ecc, lcc
N/A
Intel(R) oneAPI Math Kernel Library (oneMKL)
Mathematical Library, Optimized Computations, Thread-Safe Functions
Computer Science
Computational Software
Documentation, Uses, and more
mkl32
lcc
N/A
The Intel® oneAPI Math Kernel Library (oneMKL) helps you achieve maximum performance with a math computing library of highly optimized, extensively parallelized routines for CPU and GPU. The library has C and Fortran interfaces for most routines on CPU, and SYCL interfaces for some routines on both CPU and GPU.
Description Source: https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html#gs.4ofwv10
Mathematics, Computational Software, Hpc Tools
Other Mathematics
Library
Documentation, Uses, and more
ml-collections
lcc
1.0
A library that provides a collection of utilities for managing configurations in machine learning projects.
Machine Learning, Configuration Management, Python
Machine Learning, Artificial Intelligence and Intelligent Systems
Library
Documentation, Uses, and more
mmg
lcc
N/A
MMG is a software package designed for the generation and adaptation of unstructured meshes in two and three dimensions. It is particularly useful for numerical simulations in scientific computing.
mesh generation, mesh adaptation, scientific computing, numerical simulations
Numerical Methods, Computational Science
Open Source
Documentation, Uses, and more
mmseqs2
lcc
1.0
Mmseqs2 is a software suite to search and cluster huge protein and nucleotide sequence sets.
Sequence Searching, Sequence Clustering, Bioinformatics, Computational Biology
Biological Sciences
Sequence Search & Clustering Tool
Documentation, Uses, and more
moose
lcc
1.0
MOOSE (Multiphysics Object-Oriented Simulation Environment) is a finite element simulation framework designed for solving complex multiphysics and multiscale engineering problems. It provides a flexible and extensible platform for researchers and engineers to develop and deploy simulation tools for a wide range of applications.
Simulation, Multiphysics, Finite Element Method
Engineering & Technology
Computational Software
Documentation, Uses, and more
mosdepth
mcc
1.0
mosdepth is a tool for calculating the depth of coverage from sequencing data, particularly useful in genomic studies.
genomics, bioinformatics, sequencing, coverage
Bioinformatics, Biological Sciences
Command Line Tool
Documentation, Uses, and more
mothur
lcc, mcc
1.0
Mothur is an open source software package for bioinformatics data processing.
Bioinformatics, Microbial Communities, High-Throughput Sequencing
Microbial Ecology, Biological Sciences
Analysis Tool
Documentation, Uses, and more
mpdaf
lcc
1.0
Mpdaf is a Python package designed for the analysis of astronomical data, particularly for the processing of multi-dimensional data cubes.
Astronomy, Data Analysis, Python, Astrophysics
Astrophysics, Astronomy and Planetary Sciences
Library
Documentation, Uses, and more
mpdaf-3.5-fitsio
lcc
1.0
Documentation, Uses, and more
mpfr
ecc, lcc
N/A
The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. MPFR has continuously been supported by the INRIA and the current main authors come from the Caramba and AriC project-teams at Loria (Nancy, France) and LIP (Lyon, France) respectively; see more on the credit page. MPFR is based on the GMP multiple-precision library.
Description Source: https://www.mpfr.org/
Arbitrary-Precision Arithmetic, Floating-Point Computation, Mathematical Library
Numerical Analysis, Mathematics
Computational Software
Documentation, Uses, and more
mpi
ecc, lcc
N/A
Intel(R) MPI Library
Hpc, Parallel Computing, Message Passing, Scalable Computing
Computer Science, Computer & Information Sciences
Library
Documentation, Uses, and more
mpi4py
mcc
1.0
Mpi4py provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI specification and exposes an API which grounds on the standard MPI-2 C++ bindings.
Description Source: https://pypi.org/project/mpi4py/
Parallel Computing, Message Passing Interface, Python Library
Computer Science, Computer & Information Sciences, Other Computer & Information Sciences
Python Library
Documentation, Uses, and more
mpich
ecc, lcc
N/A
MPICH MPI implementation
Mpi Implementation, Parallel Computing, High Performance Computing
Computer Science, Computer & Information Sciences
Library
Documentation, Uses, and more
mpip
lcc
N/A
mpiP: a lightweight profiling library for MPI applications.
Software Utility, Hpc, Mpi Libraries, Cluster Management, Installation Tool
Engineering & Technology
Documentation, Uses, and more
mrbayes
lcc, mcc
1.0
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
Bayesian Inference, Phylogenetics, Evolutionary Biology
Systematics & Population Biology, Biological Sciences
Software Tool
Documentation, Uses, and more
multiqc
mcc
1.0
Multiqc is a reporting tool that parses summary statistics from results and log files generated by other bioinformatics tools.
Bioinformatics, Computational Biology, Data Analysis, Reporting Tool
Biological Sciences
Visualization Tool
Documentation, Uses, and more
mumax3
lcc
1.0
mumax3 is a GPU-accelerated micromagnetic simulation software designed for simulating the dynamics of magnetic materials.
micromagnetics, GPU computing, simulation, magnetic materials
Condensed Matter Physics
Simulation Software
Documentation, Uses, and more
mummer4
lcc
1.0
Mummer4 is a versatile alignment tool for DNA and protein sequences.
Bioinformatics, Sequence Alignment, Genomics
Genomics, Biological Sciences
Alignment Tool
Documentation, Uses, and more
mumps
lcc
N/A
A MUltifrontal Massively Parallel Sparse direct Solver
Linear Algebra, Sparse Matrices, Computational Science, Engineering
Applied Mathematics, Mathematics
Solver
Documentation, Uses, and more
muscle
lcc, mcc
1.0
Muscle is a modified progressive alignment algorithm which has comparable accuracy to MAFFT, but faster performance.
Sequence Alignment, Bioinformatics
Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
mvapich2
lcc
N/A
OSU MVAPICH2 MPI implementation
Mpi Implementation, High Performance Computing, Infiniband, Open-Source
Computer Science, Physical Sciences
Library/Tool
Documentation, Uses, and more
mvip
mcc
1.0
Documentation, Uses, and more
mvp
mcc
1.0
Documentation, Uses, and more
namd
lcc
1.0
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Molecular Dynamics, Biomolecular Systems, Parallel Computing, Cuda, Simulation
Biochemistry and Molecular Biology
Computational Software
Documentation, Uses, and more
nanocomp
mcc
1.0
Documentation, Uses, and more
nanofilt
mcc
1.0
Nanofilt is a tool for filtering and trimming of Oxford Nanopore Sequencing data.
Bioinformatics, Sequence Analysis, Nanopore Sequencing
Bioinformatics, Biological Sciences
Tool
Documentation, Uses, and more
nanogcg
lcc
1.0
Documentation, Uses, and more
nanoplot
mcc
1.0
Nanoplot is a plotting tool for long read sequencing data and alignments.
Bioinformatics, Genomics, Sequencing Data, Quality Control, Visualization
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
nanostat
mcc
1.0
Documentation, Uses, and more
nasm
lcc
N/A
Netwide Assembler (NASM) is an asssembler for the x86 CPU architecture portable to nearly every modern platform with code generation for many platforms old and new.
Description Source: https://www.nasm.us/
Assembler, Cross-Platform, X86, Programming
Computer Science, Computer & Information Sciences
Assembler
Documentation, Uses, and more
ncbi-blast+
lcc
1.0
NCBI BLAST+ is a set of command-line tools for comparing biological sequences, allowing users to find regions of similarity between sequences.
bioinformatics, sequence analysis, genomics, computational biology
Computational Biology, Bioinformatics
Command-line tool
Documentation, Uses, and more
ncl
lcc
1.0
NCL is an interpreted language designed specifically for scientific data analysis and visualization.
Scientific Data Analysis, Data Visualization, Atmospheric Sciences
Environmental Sciences, Earth & Environmental Sciences
Scripting Language
Documentation, Uses, and more
ncurses
ecc, lcc
N/A
The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.
Programming Library, Text-Based User Interfaces, Terminal Applications
Computer Science, Computer & Information Sciences
Programming/Development
Documentation, Uses, and more
ncurses-devel
lcc, mcc
1.0
Development libraries and header files for the ncurses library, which provides functions to create text-based user interfaces in a terminal.
C, Library, Text User Interface, Terminal
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
ncview
lcc
1.0
Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. It runs on UNIX platforms under X11, R4 or higher. \r
Description Source: https://cirrus.ucsd.edu/ncview/
Data Visualization, Netcdf, Earth System Data
Earth and Environmental Sciences
Data Analysis Tool
Documentation, Uses, and more
netcdf
lcc
N/A
NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
Scientific Data, Data Storage, Data Access, Data Formats, Data Manipulation, Data Visualization
Environmental Data, Other Natural Sciences
Library
Documentation, Uses, and more
netcdf-cxx
lcc
N/A
C++ Libraries for the Unidata network Common Data Form
Netcdf, C++
Earth & Environmental Sciences
Data Processing
Documentation, Uses, and more
netcdf-fortran
lcc
N/A
NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
Scientific Data, Fortran Interface, Netcdf Library
Data Analysis, Other Natural Sciences
Programming Interface
Documentation, Uses, and more
netifaces
mcc
1.0
A Python library for getting network interface information.
Networking, Python, Library
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
netlib-scalapack
lcc
N/A
ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines. ScaLAPACK solves dense and banded linear systems, least squares problems, eigenvalue problems, and singular value problems.
Description Source: https://www.netlib.org/scalapack/
linear algebra, parallel computing, high-performance computing, distributed systems
Numerical Analysis, Applied Mathematics
Library
Documentation, Uses, and more
networkx
lcc, mcc
1.0
NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
Description Source: https://networkx.org/
Python Library, Graph Theory, Network Analysis, Data Visualization
Computer & Information Sciences
Computational Software
Documentation, Uses, and more
nextflow
lcc
1.0
Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.
Description Source: https://www.nextflow.io/
Workflow Manager, Computational Biology, Data Science
Computational Biology, Biological Sciences
Open Source
Documentation, Uses, and more
ngenomesyn
mcc
1.0
Documentation, Uses, and more
nghttp2
ecc
N/A
This is an implementation of the Hypertext Transfer Protocol version 2 in C. The framing layer of HTTP/2 is implemented as a reusable C library. On top of that, we have implemented an HTTP/2 client, server and proxy. We have also developed load test and benchmarking tools for HTTP/2. An HPACK encoder and decoder are available as a public API.
Http/2, Web Protocol, Networking
Computer Science, Computer & Information Sciences
Library
Documentation, Uses, and more
nginx
lcc
1.0
nginx is a high-performance HTTP server and reverse proxy, as well as an IMAP/POP3 proxy server.
Web Server, Reverse Proxy, Load Balancer, Open Source
Computer Science
Web Server
Documentation, Uses, and more
ngsdist
lcc
1.0
ngsDist is a program for estimating pairwise genetic distances while explicitly accounting for uncertainty in genotype assignment. Instead of relying on traditional genotype calling, it operates directly on genotype likelihoods or posterior probabilities.
Documentation, Uses, and more
ngsld
mcc
1.0
ngsLD is a program to estimate pairwise linkage disequilibrium (LD) taking the uncertainty of genotype's assignation into account.
Ngs, Bioinformatics, Genomics, Sequencing
Genetics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
ngstools
lcc
1.0
Documentation, Uses, and more
ngsutils
lcc
1.0
Ngsutils is suite of software tools for working with next-generation sequencing datasets.
Ngs, Bioinformatics, Sequencing, Data Analysis
Bioinformatics, Biological Sciences
Research Tools
Documentation, Uses, and more
ninja
ecc, lcc, mcc
1.0
Ninja is a small build system with a focus on speed. It differs from other build systems in two major respects: it is designed to have its input files generated by a higher-level build system, and it is designed to run builds as fast as possible.
Description Source: https://github.com/ninja-build/ninja
Build System, Software Development, Automation
Software Engineering, Systems & Development, Engineering & Technology
Utility
Documentation, Uses, and more
ninja-build
lcc
1.0
Ninja is a small build system with a focus on speed. It is designed to be used as a backend for other build systems, and it is particularly efficient for incremental builds.
build system, automation, performance, incremental builds
Computer Science, Software Engineering
Build System
Documentation, Uses, and more
nltk
ecc
1.0
Natural Language Toolkit Description Source: https://github.com/conda-forge/nltk-feedstock/blob/main/recipe/meta.yaml
Python Library, Text Processing, Natural Language Processing
Informatics, Analytics & Information Science, Computer & Information Sciences
Text Analysis
Documentation, Uses, and more
nonpareil
mcc
1.0
Nonpareil is a software tool designed for the analysis of metagenomic data, specifically for estimating the completeness of metagenome assemblies.
metagenomics, assembly analysis, bioinformatics
Bioinformatics, Biological Sciences
Analysis Tool
Documentation, Uses, and more
notebook
ecc, lcc, mcc
1.0
Documentation, Uses, and more
novoplasty
lcc
1.0
Novoplasty is a software tool designed for de novo assembly of genomes from next-generation sequencing data, particularly focusing on the assembly of mitochondrial genomes.
bioinformatics, genomics, assembly, next-generation sequencing
Bioinformatics, Genomics
Assembly Tool
Documentation, Uses, and more
nri-md
lcc
1.0
Documentation, Uses, and more
ntlink
mcc
1.0
Documentation, Uses, and more
numactl
lcc
1.0
The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.
Numa, Memory Management, Performance Optimization
Other Computer & Information Sciences, Engineering & Technology
Tool
Documentation, Uses, and more
numactl-devel
lcc, mcc
1.0
Development files for the numactl library, which provides support for Non-Uniform Memory Access (NUMA) policies in Linux.
NUMA, Linux, Memory Management, Performance Optimization
Computer Science
Library
Documentation, Uses, and more
numactl-libs
lcc
1.0
numactl-libs provides libraries for managing Non-Uniform Memory Access (NUMA) policies in applications, allowing for better memory allocation and process management on multi-processor systems.
NUMA, Memory Management, Performance Optimization
Computer Science
Library
Documentation, Uses, and more
numba
mcc
1.0
Numba is an open source JIT compiler that translates a subset of Python and NumPy code into fast machine code.
Description Source: https://numba.pydata.org/
Jit Compiler, Python Optimization, Numpy Optimization
Computer Science, Computer & Information Sciences
Open-Source
Documentation, Uses, and more
numpy
ecc, lcc, mcc
1.0
NumPy is the fundamental package for scientific computing in Python. It is a Python library that provides a multidimensional array object, various derived objects (such as masked arrays and matrices), and an assortment of routines for fast operations on arrays, including mathematical, logical, shape manipulation, sorting, selecting, I/O, discrete Fourier transforms, basic linear algebra, basic statistical operations, random simulation and much more.
Description Source: https://numpy.org/doc/stable/user/whatisnumpy.html
Scientific Computing, Numerical Computing, Data Analysis, Mathematics
Mathematics, Computer & Information Sciences
Computational Software
Documentation, Uses, and more
nvidia-rapids
lcc
1.0
The RAPIDS data science framework is a collection of libraries for running end-to-end data science pipelines completely on the GPU. The interaction is designed to have a familiar look and feel to working in Python, but utilizes optimized NVIDIA CUDA primitives and high-bandwidth GPU memory under the hood.
GPU Computing,Data Science,Machine Learning,Open Source
Data Analytics, Computer Science
Library
Documentation, Uses, and more
nwchem
mcc
1.0
NWChem provides many methods for computing the properties of molecular and periodic systems using standard quantum mechanical descriptions of the electronic wavefunction or density. Its classical molecular dynamics capabilities provide for the simulation of macromolecules and solutions, including the computation of free energies using a variety of forcefields. These approaches may be combined to perform mixed quantum-mechanics and molecular-mechanics simulations. \r
Description Source: https://raw.githubusercontent.com/wiki/nwchemgit/nwchem/Capabilities.md
Computational Chemistry, High-Performance Computing, Open-Source Software
Chemical Sciences
Computational Chemistry Software
Documentation, Uses, and more
ocl-icd-opencl-dev
lcc
1.0
OpenCL Installable Client Driver (ICD) Loader Development Package.
OpenCL, HPC, GPU Computing, Software Development
Computer Science, Software Engineering
Library
Documentation, Uses, and more
oclfpga
lcc
N/A
The Intel® oneAPI DPC++/C++ Compiler provides optimizations that help your applications run faster on Intel® 64 architectures on Windows* and Linux*, with support for the latest C, C++, and SYCL language standards. This compiler produces optimized code that can run significantly faster by taking advantage of the ever-increasing core count and vector register width in Intel® Xeon® processors and compatible processors.
Description Source: https://www.intel.com/content/www/us/en/docs/dpcpp-cpp-compiler/get-started-guide/2024-0/overview.html
Opencl, Fpga, Acceleration
Engineering & Technology
Framework
Documentation, Uses, and more
ocr
lcc
N/A
Open Community Runtime (OCR) for shared memory
Documentation, Uses, and more
octopus
lcc
1.0
Octopus is a software package designed for the simulation of quantum systems, particularly in the field of condensed matter physics. It allows for the study of various physical phenomena using time-dependent density functional theory (TDDFT) and other quantum mechanical methods.
Quantum Mechanics, Condensed Matter Physics, Simulation Software
Physics, Physical Sciences
Simulation
Documentation, Uses, and more
ohpc
ecc, lcc
N/A
OpenHPC is a collaborative, community-driven effort to provide a comprehensive and cohesive open-source HPC stack to the community. Through close collaboration with key stakeholders across the industry, OpenHPC aims to provide a reference collection of open-source HPC software components and best practices to enable the development, testing, and deployment of HPC systems. Ultimately, building on the resecarch outputs from various related fields.
Hpc, High Performance Computing, Open-Source, Collaborative, Community-Driven
Computer Science, Engineering & Technology
Computational Software
Documentation, Uses, and more
ollama
lcc
1.0
Ollama is a free, open-source tool developed by Meta that allows users to run large language models (LLMs) locally, making it easier to develop and experiment with AI models without needing a cloud connection.
AI, Machine Learning, Natural Language Processing, Local Deployment
Computer Science, Machine Learning
Command Line Tool
Documentation, Uses, and more
omb
lcc
N/A
OSU Micro-benchmarks
Documentation, Uses, and more
ont-guppy-cpu_3.0.3_linux64
mcc
1.0
ONT Guppy is a basecaller for Oxford Nanopore sequencing data, designed to convert raw signal data into nucleotide sequences.
bioinformatics, sequencing, nanopore, basecalling
Bioinformatics, Genomics
Basecaller
Documentation, Uses, and more
openbabel
lcc, mcc
1.0
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
Description Source: https://openbabel.org/
Cheminformatics, Molecular Modeling, File Conversion, Open Source
Cheminformatics, Molecular Modeling
Library
Documentation, Uses, and more
openbabel311
mcc
1.0
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It facilitates the interconversion of various chemical file formats and provides a variety of tools for molecular manipulation.
Chemistry, File Conversion, Molecular Modeling, Open Source
Chemical Sciences, Chemical Informatics
Library
Documentation, Uses, and more
openblas
lcc
N/A
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
Linear Algebra, Blas Library, Optimized Functions, Open Source
Mathematics, Computer & Information Sciences
Library
Documentation, Uses, and more
openblas-devel
lcc
1.0
OpenBLAS is an optimized BLAS (Basic Linear Algebra Subprograms) library based on GotoBLAS2. It provides high-performance implementations of basic linear algebra operations.
BLAS, Linear Algebra, High Performance Computing, Numerical Libraries
Numerical Analysis, Applied Mathematics
Library
Documentation, Uses, and more
opencoarrays
lcc
N/A
ABI to leverage the parallel programming features of the Fortran 2018 DIS
Fortran, Parallel Computing, Coarrays, High Performance Computing
Computer Science
Library
Documentation, Uses, and more
opencv-python
ecc
1.0
OpenCV is an open-source computer vision and machine learning software library. It provides a common infrastructure for computer vision applications and to accelerate the usage of machine perception in commercial products.
Computer Vision, Image Processing, Machine Learning, Open Source
Computer Science, Artificial Intelligence and Intelligent Systems
Library
Documentation, Uses, and more
openfoam
lcc
N/A
OpenFOAM is the free, open source CFD software developed primarily by OpenCFD Ltd since 2004. It has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.
Description Source: https://www.openfoam.com/
Computational Fluid Dynamics, Open-Source Software, Finite Volume Method, Hpc
Fluid Dynamics, Physical Sciences
Computational Software
Documentation, Uses, and more
openjdk
ecc, lcc, mcc
1.0
OpenJDK is a free, Open-Source version of the Java Development Kit for the Java Platform, Standard Edition (Java SE).
Description Source: https://openjdk.org/
Open-Source, Java Development, Software Development, Programming
Software Engineering, Computer & Information Sciences
Compiler
Documentation, Uses, and more
openmm
mcc
1.0
OpenMM is a high-performance toolkit for molecular simulation. Use it as an application, a library, or a flexible programming environment. We include extensive language bindings for Python, C, C++, and even Fortran.
Description Source: https://openmm.org/
Molecular Dynamics, Biomolecular Simulations, Computational Chemistry, Biophysics, Gpu Acceleration
Bioinformatics, Biological Sciences
Molecular Dynamics Software
Documentation, Uses, and more
openmpi
lcc, mcc
1.0
The Open MPI Project is an open source MPI-3 implementation.
Mpi Library, Parallel Computing, High Performance Computing, Distributed Memory System
Computer Science, Computer & Information Sciences
Development Tools
Documentation, Uses, and more
openmpi-devel
lcc, mcc
1.0
Open MPI is a high-performance message passing library designed for parallel computing. The 'devel' package includes development files necessary for building applications that use Open MPI.
HPC, Parallel Computing, Message Passing, Open Source
Computer Science
Library
Documentation, Uses, and more
openmpi3
lcc
N/A
A powerful implementation of MPI
MPI, Parallel Computing, High Performance Computing, Cluster Computing
Computer Science
Library
Documentation, Uses, and more
openmpi4
lcc
N/A
A powerful implementation of MPI
HPC, Parallel Computing, Message Passing, Distributed Systems
Computer Science
Library
Documentation, Uses, and more
openmpi5
ecc
N/A
A powerful implementation of MPI/SHMEM
HPC, MPI, Parallel Computing, Open Source
Computer Science
Library
Documentation, Uses, and more
openpyxl
ecc
1.0
openpyxl is a Python library for reading and writing Excel (xlsx) files. It allows for the manipulation of Excel spreadsheets, enabling users to create, modify, and extract data from Excel files programmatically.
Python, Excel, Spreadsheet, Data Manipulation, Open Source
Computational Sciences, Computer Science
Library
Documentation, Uses, and more
openssh
lcc
N/A
OpenSSH is the premier connectivity tool for remote login with the SSH protocol. It encrypts all traffic to eliminate eavesdropping, connection hijacking, and other attacks. In addition, OpenSSH provides a large suite of secure tunneling capabilities, several authentication methods, and sophisticated configuration options.
Description Source: https://www.openssh.com/
Ssh, Secure Networking, Utilities
Computer Science, Computer & Information Sciences
Utility
Documentation, Uses, and more
openssh-clients
lcc
1.0
OpenSSH clients provide secure shell (SSH) protocol for secure remote login and other secure network services.
SSH, Networking, Security, Remote Access
Networking, Computer Science
Networking Tool
Documentation, Uses, and more
openssl
ecc, lcc, mcc
1.0
OpenSSL software is a robust, commercial-grade, full-featured toolkit for general-purpose cryptography and secure communication.
Description Source: https://www.openssl.org/
Cryptography, Security, Encryption, Networking
Cryptography, Computer & Information Sciences, Other Computer & Information Sciences
Toolkit
Documentation, Uses, and more
openssl-devel
lcc, mcc
1.0
Development libraries and header files for OpenSSL, a robust toolkit for implementing secure communication protocols.
Cryptography, Security, Networking, Open Source
Computer Science
Library
Documentation, Uses, and more
operams
lcc, mcc
1.0
Documentation, Uses, and more
optparse
lcc, mcc
1.0
Optparse is a Python module for parsing command-line options and arguments. It provides a flexible way to handle command-line interfaces in Python scripts.
Python, Command-line, Argument parsing
Software Engineering, Applied Computer Science
Library
Documentation, Uses, and more
orthofinder
mcc
1.0
Orthofinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplication events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.
Bioinformatics, Phylogenomics, Orthology, Gene Set Inference
Bioinformatics, Biological Sciences
Genome Analysis Software
Documentation, Uses, and more
orthologer
mcc
1.0
Documentation, Uses, and more
os
ecc
N/A
The os module in Python provides a way of using operating system dependent functionality like reading or writing to the file system.
Python, Operating System, File Management
Software Engineering, Computer Science
Library
Documentation, Uses, and more
p7zip
ecc
N/A
p7zip is a port of 7za.exe for POSIX systems like Unix (Linux, Solaris, OpenBSD, FreeBSD, Cygwin, AIX, ...), MacOS X and also for BeOS and Amiga.
Description Source: https://p7zip.sourceforge.net/
File Archiver, Compression Software, Command-Line Tool, Open-Source Software
Computer Science, Computer & Information Sciences
Command-line Tool
Documentation, Uses, and more
paml
lcc
1.0
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It may be used to estimate parameters and test hypotheses to study the evolutionary process.
Description Source: http://abacus.gene.ucl.ac.uk/software/paml.html
Phylogenetics, Evolutionary Analysis, Maximum Likelihood, Phylogenetic Inference
Genetics, Biological Sciences
Computational Software
Documentation, Uses, and more
pandas
ecc, lcc, mcc
1.0
Powerful data structures for data analysis, time series, and statistics Description Source: https://github.com/conda-forge/pandas-feedstock/blob/main/recipe/meta.yaml
Python Library, Data Manipulation, Data Analysis, Structured Data, Tabular Data
Informatics, Analytics & Information Science, Computer & Information Sciences
Library
Documentation, Uses, and more
papi
lcc
N/A
Performance Application Programming Interface
Performance Monitoring, Api, Hardware Counter
Computer Science
Library
Documentation, Uses, and more
parallel
lcc, mcc
1.0
Parallel processing made simple and fast and runs any code in parallel processes(> use all CPUs), Threads(> speedup blocking operations), or Ractors(> use all CPUs).
Description Source: https://github.com/grosser/parallel
Parallel Computing, Command-Line Tool, Task Scheduling
Computer & Information Sciences
Command-Line Tool
Documentation, Uses, and more
parasail-python
mcc
1.0
A Python library for high-performance pairwise sequence alignment using SIMD instructions.
Bioinformatics, Sequence Alignment, High-Performance Computing
Bioinformatics
Library
Documentation, Uses, and more
paraview
mcc
1.0
ParaView is an open-source, multi-platform scientific data analysis and visualization tool that enables analysis and visualization of extremely large datasets.
Description Source: https://docs.paraview.org/en/latest/UsersGuide/introduction.html
Visualization, Data Analysis, Open-Source, Multi-Platform
Data Visualization, Physical Sciences, Engineering & Technology, Natural Sciences, Computer & Information Sciences, Other Natural Sciences
Data Visualization
Documentation, Uses, and more
partitionfinder
lcc
1.0
PartitionFinder is a software tool for selecting the best partitioning schemes and models of molecular evolution for phylogenetic analyses.
phylogenetics, model selection, bioinformatics
Computational Biology, Bioinformatics
Desktop Application
Documentation, Uses, and more
patch
ecc, lcc, mcc
1.0
The `patch` utility is a tool used to apply changes to files based on a diff file, which contains the differences between two versions of a file or set of files.
version control, file management, diff, software development
Software Engineering, Other Computer and Information Sciences
Command-line tool
Documentation, Uses, and more
patchelf
lcc
1.0
PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.
Dependency Management, Executable Modification, Dynamic Linker Paths
Systems and Development, Computer & Information Sciences
Library Management
Documentation, Uses, and more
pb-assembly
lcc
1.0
Documentation, Uses, and more
pbccs
lcc, mcc
1.0
Documentation, Uses, and more
pbjelly
lcc, mcc
1.0
bioinformatics, genomics, DNA assembly
Bioinformatics, Genomics
Assembly Tool
Documentation, Uses, and more
pblat
mcc
1.0
pblat is parallelized blat with multi-threads support.
Bioinformatics, Sequence Alignment, Genomics, Parallel Computing
Genomics, Biological Sciences
Sequence Analysis Tool
Documentation, Uses, and more
pbmm2
lcc, mcc
1.0
Pbmm2 is a minimap2 frontend for PacBio native data formats.
Long Read Aligner, Graph-Guided Mapping, Reference Genome Mapping, Bioinformatics
Bioinformatics, Biological Sciences
Alignment Tool
Documentation, Uses, and more
pbtk
lcc, mcc
1.0
Documentation, Uses, and more
pcangsd
mcc
1.0
PCAngsd is a program that estimates the covariance matrix and individual allele frequencies for low-depth next-generation sequencing (NGS) data in structured/heterogeneous populations using principal component analysis (PCA) to perform multiple population genetic analyses using genotype likelihoods.
Population Genetics, Genomic Data Analysis
Genetics, Biological Sciences
Tool
Documentation, Uses, and more
pciutils
lcc
1.0
pciutils is a set of utilities for displaying information about PCI buses in the system and devices connected to them. It provides various tools for configuration, diagnostics, and monitoring of PCI devices in Linux systems.
Pci Management, System Utilities, Linux Tools
Systems, Computer & Information Sciences
Command-Line Tool
Documentation, Uses, and more
pcre
lcc
1.0
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. NOTE:This version of PCRE is now at end of life, and is no longer being actively maintained. New Projects should use PCRE2 instead.
Description Source: https://www.pcre.org/
Regular Expressions, Pattern Matching, Library
Biology, Computer & Information Sciences
Runtime Library
Documentation, Uses, and more
pcre2
ecc
N/A
PCRE2 is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PCRE has its own native API, as well as a set of wrapper functions that correspond to the POSIX regular expression API. NOTE: This is the current version of the PCRE library.
Description Source: https://www.pcre.org/
Regular Expressions, Text Processing, Pattern Matching
Biology, Computer & Information Sciences
C Library
Documentation, Uses, and more
pdfminer.six
ecc
1.0
pdfminer.six is a Python library for extracting information from PDF documents. It focuses on getting and analyzing text data from PDF files, enabling users to work with PDF content programmatically.
PDF, Text Extraction, Document Analysis, Python
Computer Science, Software Engineering
Library
Documentation, Uses, and more
pdtoolkit
lcc
N/A
PDT is a framework for analyzing source code
Python Library, Exploratory Data Analysis, Data Preprocessing, Feature Selection, Visualization
Computer & Information Sciences
Python Library
Documentation, Uses, and more
pegtl
lcc
N/A
PEGTL (Parsing Expression Grammar Template Library) is a C++ library designed for parsing expression grammars, providing a framework for implementing parsers in a straightforward manner.
C++, Parsing, Grammar, Template Library
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
perl
ecc, lcc, mcc
1.0
Larry Wall's Practical Extraction and Report Language
Programming Language, Text Processing, Scripting, Web Development, System Administration
Bioinformatics, Computer & Information Sciences
Programming Language
Documentation, Uses, and more
perl-app-cpanminus
mcc
1.0
cpanminus is a script to get, unpack, build and install modules from CPAN.
Perl, CPAN, Package Manager
Software Engineering, Computer Science
Package Management
Documentation, Uses, and more
perl-bio-viennangs
mcc
1.0
Documentation, Uses, and more
perl-bioperl
lcc, mcc
1.0
BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming.
bioinformatics, perl, sequence analysis, genomics, molecular biology
Computational Biology, Biological Sciences
Library
Documentation, Uses, and more
perl-core
mcc
1.0
Perl is a high-level, general-purpose, interpreted programming language known for its text processing capabilities.
Programming Language, Scripting, Text Processing, Open Source
Computer Science, Software Engineering
Programming Language
Documentation, Uses, and more
perl-cpan
lcc
1.0
CPAN (Comprehensive Perl Archive Network) is a repository of over 250,000 Perl modules and distributions, allowing users to easily install and manage Perl software.
Perl, Package Management, Software Development
Computer Science, Software Engineering
Package Manager
Documentation, Uses, and more
perl-data-dumper
lcc
1.0
Documentation, Uses, and more
perl-devel
mcc
1.0
perl-devel is a development package for Perl, providing essential tools and libraries for building Perl modules and applications.
Perl, Development, Programming
Computer Science, Software Engineering
Development Tool
Documentation, Uses, and more
perl-file-path
lcc
1.0
Documentation, Uses, and more
perl-file-temp
lcc
1.0
perl-file-temp is a Perl module that provides a simple way to create temporary files and directories safely.
Perl, Temporary Files, File Management
Computer Science
Library
Documentation, Uses, and more
perl-getopt-long
lcc
1.0
Documentation, Uses, and more
perl-ipc-cmd
lcc
1.0
Documentation, Uses, and more
perl-ipc-run
mcc
1.0
Documentation, Uses, and more
perl-velvetoptimiser
lcc, mcc
1.0
Documentation, Uses, and more
petsc
lcc
N/A
Portable Extensible Toolkit for Scientific Computation
Scientific Computing, Computational Science, Numerical Analysis
Applied Mathematics, Natural Sciences
Library
Documentation, Uses, and more
pggb
mcc
1.0
pggb builds pangenome variation graphs from a set of input sequences.
Performance Evaluation, Benchmarking, Computational Applications
Performance Evaluation & Benchmarking, Training
Documentation, Uses, and more
phangorn
lcc
1.0
phangorn is an R package for phylogenetic analysis, providing tools for constructing and manipulating phylogenetic trees.
phylogenetics, R, bioinformatics, evolutionary biology
Computational Biology, Phylogenetics
Library
Documentation, Uses, and more
phasebook
mcc
1.0
Documentation, Uses, and more
phastest
mcc
1.0
Documentation, Uses, and more
phdf5
lcc
N/A
A general purpose library and file format for storing scientific data
Parallel I/O, Phdf5, Hdf5, Large Datasets
Computer & Information Sciences
File Format
Documentation, Uses, and more
phrynomics
mcc
1.0
Documentation, Uses, and more
phylophlan
lcc
1.0
PhyloPhlAn is a software tool for phylogenetic analysis of metagenomic data, focusing on the reconstruction of phylogenetic trees from genomic data.
bioinformatics, phylogenetics, genomics, microbiology
Microbial phylogenetics, Biological Sciences
Command-line tool
Documentation, Uses, and more
phyml
lcc
1.0
PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. PhyML was designed to process moderate to large data sets and can process data sets made of multiple genes and fit sophisticated substitution models with heterogeneous components across partition elements.
phylogenetics,bioinformatics,maximum likelihood,tree estimation
Bioinformatics, Phylogenetics
Standalone
Documentation, Uses, and more
picard
mcc
1.0
Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification.
Description Source: https://broadinstitute.github.io/picard/
Bioinformatics, Ngs, Hts, Sequencing Data, Sam, Bam, Vcf
Genomics, Biological Sciences
Command Line Tool
Documentation, Uses, and more
picrust2
mcc
1.0
Picrust2 is a software for predicting functional abundances based only on marker gene sequences.
Bioinformatics, Metagenomics, Microbiome Analysis, Functional Gene Prediction
Biological Sciences
Metagenomics Tool
Documentation, Uses, and more
pigz
ecc, lcc
N/A
pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries.
Description Source: https://zlib.net/pigz/
Compression, Parallel Processing, Utility, Command-Line Tool
Computer Science, Computer & Information Sciences
Utility
Documentation, Uses, and more
pillow
ecc
1.0
Pillow is a Python Imaging Library (PIL) fork that provides extensive image processing capabilities in Python. It allows users to create, open, manipulate, and save various image file formats, making it a versatile tool for image editing, processing, and enhancement.
Image Processing, Python Library
Applied Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development
Library
Documentation, Uses, and more
pilon
lcc
1.0
Pilon is an automated genome assembly improvement and variant detection tool.
Genome Assembly, Genomics, Bioinformatics, Computational Biology
Genomics, Biological Sciences
Tool
Documentation, Uses, and more
pip
ecc, lcc
1.0
pip is a package management system for Python that simplifies the installation and management of software packages written in Python.
Python, Package Management, Open Source
Computer Science, Software Engineering
Package Manager
Documentation, Uses, and more
pipeline
mcc
1.0
Documentation, Uses, and more
pkg-config
lcc
N/A
pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries).
Compilation, Library Management, Build Process
Computer Science, Engineering & Technology
Utility
Documentation, Uses, and more
pkgconf
ecc, lcc
N/A
pkgconf is a program which helps to configure compiler and linker flags for development frameworks. It is similar to pkg-config from freedesktop.org, providing additional functionality while also maintaining compatibility.
Description Source: http://pkgconf.org/
Package Configuration, Build Flags, Link Flags, System-Agnostic
Software Engineering, Computer & Information Sciences
Package Configuration
Documentation, Uses, and more
pkgconf-pkg-config
lcc
1.0
pkgconf is a tool that helps manage compile and link flags for libraries in a consistent manner. It is a replacement for pkg-config, providing a more modern and efficient approach to handling package metadata.
build tools, package management, development
Computer Science, Software Engineering
Library Management Tool
Documentation, Uses, and more
pkgconfig
lcc, mcc
1.0
pkgconfig is a Python module to interface with the pkg-config command line tool for Python 3.3+. It can be used to find all pkg-config packages, check if a package exists, check if a package meets certain version requirements, return the version, among other functionality.
Description Source: https://github.com/matze/pkgconfig/tree/master
Compilation, Library Management, Software Development
Software Engineering, Engineering & Technology
Tool
Documentation, Uses, and more
plascad
lcc
1.0
Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasmid visualization.
Documentation, Uses, and more
plasma
lcc
N/A
Parallel Linear Algebra Software for Multicore Architectures
Documentation, Uses, and more
plink
lcc, mcc
1.0
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
Description Source: https://zzz.bwh.harvard.edu/plink/
Genetic Analysis, Genomic Data Analysis, Gwas, Genetic Epidemiology
Genetics, Biological Sciences
Tool
Documentation, Uses, and more
plink2
mcc
1.0
Plink2 is a whole genome association analysis toolset.
Genomics, Association Analysis, Genotype-Phenotype Data
Genetics
Tool
Documentation, Uses, and more
plot3d
lcc
1.0
Documentation, Uses, and more
plotsr
mcc
1.0
Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies.
Plotting, Data Visualization, Python Library
Computer & Information Sciences
Data Visualization
Documentation, Uses, and more
plyr
lcc, mcc
1.0
plyr is an R package that provides a set of functions for data manipulation and transformation, making it easier to work with data frames and lists.
Data Manipulation, R Package, Data Science
Statistics, Applied Mathematics
Library
Documentation, Uses, and more
pmix
lcc
N/A
The Process Management Interface (PMI) has been used for quite some time as a means of exchanging wireup information needed for inter-process communication. Two versions (PMI-1 and PMI-2) have been released as part of the MPICH effort, with PMI-2 demonstrating better scaling properties than its PMI-1 predecessor.
Description Source: https://pmix.github.io/standard
Process Management, Parallel Computing, High-Performance Computing, Data Exchange, Resource Management, Scalability
Computer Science, Engineering & Technology
Hpc Tool
Documentation, Uses, and more
pnetcdf
lcc
N/A
A Parallel NetCDF library (PnetCDF)
Parallel I/O, Netcdf Files, Scalability, Performance
High-Performance Computing, Physical Sciences
I/O Library
Documentation, Uses, and more
popoolation
mcc
1.0
Popoolation is a software tool designed for the analysis of pooled next-generation sequencing data. It allows researchers to estimate allele frequencies, detect variants, and perform population genetic analyses.
bioinformatics, population genetics, next-generation sequencing
Population Genetics, Genomics
Analysis Tool
Documentation, Uses, and more
porechop
mcc
1.0
Porechop is a tool designed for the trimming of Illumina sequencing data, specifically focusing on the removal of adapter sequences and low-quality reads.
bioinformatics, sequence analysis, data processing
Bioinformatics, Genomics
Command-line tool
Documentation, Uses, and more
prank
lcc
1.0
PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events.
Sequence Alignment, Bioinformatics, Genomics, Phylogenetics
Genetics, Biological Sciences
Computational Software
Documentation, Uses, and more
prank=v.150803
lcc
1.0
PRANK is a software tool for phylogenetic analysis that implements a method for multiple sequence alignment based on a probabilistic model of evolution.
phylogenetics, sequence alignment, bioinformatics
Bioinformatics, Molecular Biology
Alignment Tool
Documentation, Uses, and more
pretext-suite
lcc, mcc
1.0
Documentation, Uses, and more
procps-ng
lcc
1.0
procps-ng is a suite of command-line utilities that provide information about processes and system resource usage in Unix-like operating systems.
System Monitoring, Process Management, Unix Utilities
Operating Systems, Other Computer and Information Sciences
Command-line Tool
Documentation, Uses, and more
prodigal
mcc
1.0
Prodigal (PROkaryotic DynamIc programming Genefinding ALgorithm) is an open source lightweight microbial genefinding program developed at University of Tennessee and Oak Ridge National Laboratory.
Description Source: https://www.psc.edu/resources/software/prodigal/
Gene Prediction, Microbial Genomes
Biological Sciences
Bioinformatics
Documentation, Uses, and more
prodigal-2.6.3
mcc
1.0
Documentation, Uses, and more
prody
lcc
1.0
ProDy is a Python package for protein dynamics analysis that allows users to perform various analyses on molecular dynamics simulations and structural data.
bioinformatics, computational biology, protein dynamics, molecular modeling
Bioinformatics, Biophysics
Library
Documentation, Uses, and more
proj-devel
mcc
1.0
Documentation, Uses, and more
prokka
lcc
1.0
Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.
Description Source: https://github.com/tseemann/prokka
Genome Annotation, Bioinformatics, Genomics
Genetics, Biological Sciences
Annotation Tool
Documentation, Uses, and more
protobuf
lcc
N/A
Protocol Buffers are language-neutral, platform-neutral extensible mechanisms for serializing structured data.
Description Source: https://protobuf.dev/
Serialization, Data Interchange, Code Generation
Software Engineering, Computer & Information Sciences
Library
Documentation, Uses, and more
prun
ecc, lcc
N/A
job launch utility for multiple MPI families
Parallel Computing, High-Performance Computing, Distributed Computing, Data Analysis, Computation
Other Computer & Information Sciences
Computational Software
Documentation, Uses, and more
psi4
mcc
1.0
Psi4 is an open-source quantum chemistry package that provides a variety of methods for electronic structure calculations, including Hartree-Fock, post-Hartree-Fock, and density functional theory (DFT).
Quantum Chemistry, Electronic Structure, Computational Chemistry, Open Source
Theoretical Chemistry, Quantum Chemistry
Scientific Software
Documentation, Uses, and more
psutil
mcc
1.0
psutil is a cross-platform library for process and system monitoring in Python. It provides an interface for retrieving information on running processes and system utilization (CPU, memory, disks, network, sensors) in a portable way.
Python, Monitoring, System Utilities, Cross-Platform
Applied Computer Science, Other Computer and Information Sciences
Library
Documentation, Uses, and more
ptscotch
lcc
N/A
Graph, mesh and hypergraph partitioning library using MPI
Graph Partitioning, Parallel Computing, High Performance Computing, Scientific Computing
Computer Science, Applied Computer Science
Library
Documentation, Uses, and more
pugixml
lcc
N/A
pugixml is a light-weight C++ XML processing library
Xml Processing, C++ Library, Xpath, Parsing
Software Engineering, Computer & Information Sciences
Xml Processing
Documentation, Uses, and more
pulp
mcc
1.0
PuLP is a Python library for modeling linear programming problems. It allows users to describe optimization problems in a natural way and provides a simple interface to various solvers.
Optimization, Linear Programming, Mathematics, Python
Optimization, Mathematics
Library
Documentation, Uses, and more
purge_dups
mcc
1.0
purge_dups is designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.
Bioinformatics, Genomics, DNA Sequences
Genomics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
py-cython
ecc
N/A
Py-Cython is a compiler for writing C extensions for the Python language. It allows for combining Python and C code seamlessly to improve performance and efficiency.
Compiler, Python Library, Performance Optimization
Computer & Information Sciences
Development Tool
Documentation, Uses, and more
py-mako
lcc
N/A
Mako is a fast and lightweight templating engine for Python, designed to be easy to use and integrate with existing applications.
templating, Python, web development
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
py-markupsafe
lcc
N/A
A library for safe string handling in Python, particularly for HTML and XML.
Python, String Handling, Web Development
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
py-pip
ecc, lcc
N/A
py-pip is the official installer for Python packages from the Python Package Index (PyPI). It is used to install and manage software packages written in Python.
Package Management, Python, Software Installation
Software Engineering, Computer & Information Sciences, Systems & Development
Package Management
Documentation, Uses, and more
py-setuptools
ecc, lcc
N/A
Setuptools is a package development process library designed to facilitate development and distribution of Python projects. It provides a common approach for managing project dependencies, packaging, and installation processes.
Python, Package Development, Distribution, Dependency Management
Computer Science, Computer & Information Sciences
Package Management
Documentation, Uses, and more
py-wheel
ecc, lcc
N/A
Documentation, Uses, and more
py2-mpi4py
lcc
N/A
Python bindings for the Message Passing Interface (MPI) standard.
Documentation, Uses, and more
py2-numpy
lcc
N/A
NumPy array processing for numbers, strings, records and objects
Documentation, Uses, and more
py2-scipy
lcc
N/A
Scientific Tools for Python
Documentation, Uses, and more
py3-mpi4py
lcc
N/A
Python bindings for the Message Passing Interface (MPI) standard.
MPI, Python, Parallel Computing, High Performance Computing
High-Performance Computing, Computer Science
Library
Documentation, Uses, and more
py3-numpy
lcc
N/A
NumPy array processing for numbers, strings, records and objects
Python, Scientific Computing, Numerical Analysis, Data Science
Mathematics, Applied Mathematics
Library
Documentation, Uses, and more
py3-scipy
lcc
N/A
Scientific Tools for Python
Python, Scientific Computing, Numerical Analysis, Data Science
Applied Mathematics, Computer Science
Library
Documentation, Uses, and more
py4vasp
mcc
1.0
py4vasp is a Python package designed to facilitate the analysis and visualization of VASP (Vienna Ab initio Simulation Package) output files. It provides tools for extracting relevant data from VASP calculations and generating plots and other visualizations to aid in the interpretation of results.
Python, VASP, Computational Chemistry, Data Analysis, Visualization
Computational Chemistry, Physical Chemistry
Library
Documentation, Uses, and more
pyamg
mcc
1.0
pyamg is a Python library for solving large sparse linear systems using algebraic multigrid methods.
linear algebra, multigrid, sparse matrices, scientific computing
Numerical Analysis, Applied Mathematics
Library
Documentation, Uses, and more
pyani
mcc
1.0
Pyani is an application and Python module for whole-genome classification of microbes using Average Nucleotide Identity.
Bioinformatics, Computational Biology, Microbial Genomics
Bioinformatics, Biological Sciences
Genomics Tool
Documentation, Uses, and more
pyani-0.2.13.1
mcc
1.0
pyani is a Python package for calculating average nucleotide identity (ANI) between microbial genomes.
bioinformatics, genomics, sequence analysis
Microbiology, Bioinformatics
Library
Documentation, Uses, and more
pyarrow
lcc
1.0
Documentation, Uses, and more
pybind11
lcc
1.0
pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. Its goals and syntax are similar to the excellent Boost.Python library by David Abrahams: to minimize boilerplate code in traditional extension modules by inferring type information using compile-time introspection.
Description Source: https://github.com/pybind/pybind11
Software Development, Python Library, C++ Integration, Header-Only Library
Software Engineering, Computer & Information Sciences
Interoperability
Documentation, Uses, and more
pydub
ecc
1.0
pydub is a Python library for audio manipulation, allowing users to easily work with audio files, including tasks such as slicing, concatenating, and applying effects.
audio processing, Python, sound manipulation, music analysis
Applied Computer Science, Informatics
Library
Documentation, Uses, and more
pymatgen
mcc
1.0
Pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis and manipulation, particularly for computational materials science.
materials science, computational chemistry, data analysis, python
Computational Materials Science, Materials Science
Library
Documentation, Uses, and more
pymeshlab
lcc, mcc
1.0
PyMeshLab is a Python binding for the MeshLab software, allowing users to manipulate and process 3D meshes programmatically.
3D modeling, Mesh processing, Computer graphics, Scientific computing
3D Mesh Processing, Computer Science
Library
Documentation, Uses, and more
pymupdf
ecc
1.0
PyMuPDF is a Python binding for MuPDF, a lightweight PDF and XPS viewer. It allows for the manipulation of PDF documents, including reading, writing, and rendering.
PDF, Document Processing, Rendering, Text Extraction, Image Processing
Software Engineering, Applied Computer Science
Library
Documentation, Uses, and more
pysam
lcc, mcc
1.0
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
Description Source: https://github.com/pysam-developers/pysam
Bioinformatics, Sequence Analysis, Sam/Bam Files, Python Module
Bioinformatics, Biological Sciences
Library
Documentation, Uses, and more
pytesseract
ecc
1.0
Python-tesseract is an optical character recognition (OCR) tool for python. That is, it will recognize and “read” the text embedded in images. Python-tesseract is a wrapper for Google’s Tesseract-OCR Engine. It is also useful as a stand-alone invocation script to tesseract, as it can read all image types supported by the Pillow and Leptonica imaging libraries, including jpeg, png, gif, bmp, tiff, and others.
Description Source: https://pypi.org/project/pytesseract/
Ocr, Text Recognition, Image Processing
Artificial Intelligence, Computer & Information Sciences
Ocr Library
Documentation, Uses, and more
pytest
mcc
1.0
The pytest framework makes it easy to write small, readable tests, and can scale to support complex functional testing for applications and libraries.
Description Source: https://docs.pytest.org/en/8.0.x/
Testing, Python, Framework
Computer Science, Computer & Information Sciences
Testing Framework
Documentation, Uses, and more
python
ecc, lcc, mcc
1.0
Python is an interpreted, interactive, object-oriented programming language. It incorporates modules, exceptions, dynamic typing, very high level dynamic data types, and classes. It supports multiple programming paradigms beyond object-oriented programming, such as procedural and functional programming. Python combines remarkable power with very clear syntax. It has interfaces to many system calls and libraries, as well as to various window systems, and is extensible in C or C++. It is also usable as an extension language for applications that need a programmable interface. Finally, Python is portable: it runs on many Unix variants including Linux and macOS, and on Windows.
Description Source: https://docs.python.org/3/faq/general.html#what-is-python
Programming Language, Interpreted Language, High-Level Language
Software Engineering, Computer & Information Sciences, Systems & Development
Language
Documentation, Uses, and more
python-annoy
lcc
1.0
Annoy (Approximate Nearest Neighbors Oh Yeah) is a C++ library with Python bindings that is designed to find approximate nearest neighbors in high-dimensional spaces. It is particularly useful for recommendation systems and other machine learning applications.
Machine Learning, Data Science, Approximate Nearest Neighbors, High-Dimensional Data
Computer Science, Artificial Intelligence and Intelligent Systems
Library
Documentation, Uses, and more
python-dev
mcc
1.0
Documentation, Uses, and more
python-devtools
mcc
1.0
Documentation, Uses, and more
python-pip
lcc, mcc
1.0
Python pip is a package manager for Python that allows users to install and manage software packages written in Python.
Python, Package Management, Development Tools
Computer Science, Software Engineering
Package Manager
Documentation, Uses, and more
python-venv
ecc
N/A
A tool for creating isolated Python environments, allowing users to manage dependencies for different projects independently.
Python, Virtual Environment, Dependency Management
Computer Science, Software Engineering
Library
Documentation, Uses, and more
python3
lcc, mcc
1.0
Python is an interpreted, interactive, object-oriented programming language. It incorporates modules, exceptions, dynamic typing, very high level dynamic data types, and classes. It supports multiple programming paradigms beyond object-oriented programming, such as procedural and functional programming. Python combines remarkable power with very clear syntax. It has interfaces to many system calls and libraries, as well as to various window systems, and is extensible in C or C++. It is also usable as an extension language for applications that need a programmable interface. Finally, Python is portable: it runs on many Unix variants including Linux and macOS, and on Windows.
Description Source: https://docs.python.org/3/faq/general.html#what-is-python
Programming Language, Scripting Language
Computer Science, Computer & Information Sciences, Other Computer & Information Sciences
Interpreter
Documentation, Uses, and more
python3-dev
lcc, mcc
1.0
The python3-dev package contains the header files and a static library for Python 3 development. It is essential for building Python modules and extensions.
Python, Development, Programming, Software Engineering
Software Engineering, Computer Science
Development Library
Documentation, Uses, and more
python3-devel
lcc, mcc
1.0
Development files for Python 3, including headers and static libraries for building Python modules.
Python, Development, Programming, Software Engineering
Software Engineering
Development Tools
Documentation, Uses, and more
python3-matplotlib
lcc
1.0
Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python.
Data Visualization, Plotting, Scientific Computing, Python
Computer Science
Library
Documentation, Uses, and more
python3-pip
lcc, mcc
1.0
Python package installer that allows users to install and manage additional libraries and dependencies not included in the standard Python distribution.
Python, Package Management, Development Tools
Computer Science, Software Engineering
Command-line tool
Documentation, Uses, and more
python3-pyqt5
mcc
1.0
PyQt5 is a set of Python bindings for The Qt Company’s Qt application framework, enabling the development of cross-platform applications with a native look and feel.
GUI, Python, Qt, Cross-platform
Computer Science, Software Engineering
Library
Documentation, Uses, and more
python3-pyqt5.qtsvg
mcc
1.0
A set of Python bindings for the Qt libraries, specifically for handling Scalable Vector Graphics (SVG) files.
Python, Qt, SVG, GUI, Cross-platform
Software Engineering, Computer and Information Sciences
Library
Documentation, Uses, and more
python3-setuptools
lcc, mcc
1.0
Setuptools is a package development and distribution tool for Python. It provides support for building and distributing Python packages, including support for dependencies, package versioning, and installation scripts.
Python, Package Management, Development Tools
Computer Science, Software Engineering
Library
Documentation, Uses, and more
python3-venv
lcc
1.0
A module for creating lightweight, isolated Python environments.
Python, Virtual Environment, Package Management
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
python312_ml
mcc
1.0
Documentation, Uses, and more
python39
lcc
1.0
Python 3.9 is a high-level, interpreted programming language known for its readability and versatility. It supports multiple programming paradigms, including procedural, object-oriented, and functional programming.
programming, scripting, open-source, interpreted
Software Engineering, Computer Science
Programming Language
Documentation, Uses, and more
python39-devel
lcc
1.0
Development files for Python 3.9, including headers and static libraries needed for building Python modules.
Python, Development, Programming, Software Engineering
Software Engineering, Computer Science
Development Tools
Documentation, Uses, and more
python39-pip
lcc
1.0
pip is the package installer for Python. It allows you to install and manage additional libraries and dependencies that are not part of the standard Python library.
Python, Package Management, Development Tools
Computer Science, Software Engineering
Package Manager
Documentation, Uses, and more
python>=3.10
mcc
1.0
Python is a high-level, interpreted programming language known for its readability and versatility, widely used in various fields including web development, data analysis, artificial intelligence, scientific computing, and more.
Programming Language, Interpreted, High-level, Open Source
Computer Science, Software Engineering
Programming Language
Documentation, Uses, and more
python>=3.7
mcc
1.0
Python is a high-level, interpreted programming language known for its readability and versatility. It supports multiple programming paradigms and is widely used in various domains including web development, data analysis, artificial intelligence, scientific computing, and more.
Programming Language, Interpreted, High-level, Open Source
Software Engineering, Computer Science
Programming Language
Documentation, Uses, and more
pytorch
lcc
1.0
PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
Description Source: https://pytorch.org/docs/stable/index.html
Machine Learning, Deep Learning, Numerical Computation, Neural Networks
Artificial Intelligence & Intelligent Systems, Computer & Information Sciences
Machine Learning Framework
Documentation, Uses, and more
pytorch-lightning
lcc
1.0
PyTorch Lightning is the deep learning framework for professional AI researchers and machine learning engineers who need maximal flexibility without sacrificing performance at scale. Lightning evolves with you as your projects go from idea to paper/production.
Description Source: https://lightning.ai/docs/pytorch/stable/
Deep Learning, Machine Learning, PyTorch, Framework
Machine Learning, Deep Learning
Python Library
Documentation, Uses, and more
pytraj
lcc, mcc
1.0
PyTraj is a Python library for analyzing molecular dynamics trajectories. It is part of the AmberTools suite and provides tools for trajectory manipulation, analysis, and visualization.
Molecular Dynamics, Bioinformatics, Computational Chemistry, Python
Molecular Dynamics, Biochemistry and Molecular Biology
Library
Documentation, Uses, and more
pyvcf
mcc
1.0
pyvcf is a Python library for parsing and manipulating VCF (Variant Call Format) files, which are commonly used in bioinformatics to store gene sequence variations.
bioinformatics, genomics, data analysis, variant calling
Genomics, Genetic Variation
Library
Documentation, Uses, and more
pyyaml
lcc
1.0
YAML is a data serialization format designed for human readability and interaction with scripting languages. PyYAML is a YAML parser and emitter for Python.
Description Source: https://pypi.org/project/PyYAML/
Yaml, Parser, Emitter
Other Computer & Information Sciences, Computer & Information Sciences
Data Serialization
Documentation, Uses, and more
qe
lcc, mcc
1.0
Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. \r
Description Source: https://www.quantum-espresso.org/
Quantum Mechanics, Materials Science, Computational Physics
Physical Sciences
Open-source
Documentation, Uses, and more
qiime2
lcc, mcc
1.0
QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. \r
Description Source: https://qiime2.org/
Microbiome, Bioinformatics, Sequencing
Bioinformatics
Analysis Software
Documentation, Uses, and more
qiime2-amplicon
lcc
1.0
QIIME 2 is an open-source bioinformatics platform for performing microbiome analysis. The amplicon plugin provides tools for analyzing amplicon sequence data.
bioinformatics, microbiome, amplicon sequencing, data analysis
Bioinformatics, Biological Sciences
Open-source
Documentation, Uses, and more
qiime2-shotgun
lcc
1.0
Documentation, Uses, and more
qiime2-tiny
lcc
1.0
Documentation, Uses, and more
qiime2amplicon
lcc
1.0
Documentation, Uses, and more
qiskit
lcc
1.0
Qiskit is an open-source quantum computing software development framework that provides tools for creating, simulating, and executing quantum programs.
Quantum Computing, Open Source, Simulation, IBM
Quantum Computing, Quantum Algorithms
Library
Documentation, Uses, and more
qiskit-aer-gpu
lcc
1.0
Qiskit Aer is a high-performance simulator for quantum circuits, and the GPU version leverages graphics processing units to accelerate simulations.
Quantum Computing, Simulation, GPU Acceleration, High-Performance Computing
Quantum Information Science, Quantum Computing
Simulation Software
Documentation, Uses, and more
qtbase5-dev
mcc
1.0
Qt Base Development Libraries provide the core non-GUI functionality of the Qt framework, including event handling, file handling, and data structures.
C++, GUI, Cross-platform, Development, Framework
Software Engineering
Library
Documentation, Uses, and more
quantum-espresso
lcc, mcc
1.0
Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
Description Source: https://www.quantum-espresso.org/
Quantum Mechanics, Materials Science, Computational Physics
Chemistry, Condensed Matter Physics
Package
Documentation, Uses, and more
quantumespresso
lcc
1.0
Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
Description Source: https://www.quantum-espresso.org/
Quantum Mechanics, Materials Science, Computational Physics
Chemistry, Condensed Matter Physics
Package
Documentation, Uses, and more
quast
lcc
1.0
Quast is Quality Assessment Tool for Genome Assemblies.
Genome Assembly, Bioinformatics, Quality Assessment
Genomics, Biological Sciences
Stand-Alone Tool
Documentation, Uses, and more
quorum
lcc
1.0
Documentation, Uses, and more
lcc, mcc
1.0
R is a language and environment for statistical computing and graphics (S-Plus like).
Statistical Computing, Data Analysis, Statistical Graphics
Computer Science
Statistical Software
Documentation, Uses, and more
r-base
lcc, mcc
1.0
R is a programming language and free software environment for statistical computing and graphics supported by the R Foundation for Statistical Computing.
Statistics, Data Science, Visualization, Open Source
Statistics, Statistical Computing
Programming Language
Documentation, Uses, and more
r-fastbaps
lcc
1.0
Documentation, Uses, and more
r-peer
lcc
1.0
Documentation, Uses, and more
r-plm
lcc
1.0
r-plm is an R package designed for fitting linear models with a focus on panel data. It provides tools for estimating fixed effects, random effects, and other models suitable for longitudinal data analysis.
R, Statistics, Panel Data, Econometrics
Statistics, Econometrics
Library
Documentation, Uses, and more
r-plm-1.6_5
lcc
1.0
Documentation, Uses, and more
r-seurat
mcc
1.0
Seurat is an R package designed for single-cell RNA sequencing data analysis, providing tools for data normalization, clustering, and visualization.
bioinformatics, single-cell analysis, R package, data visualization
Bioinformatics, Biochemistry and Molecular Biology
Library
Documentation, Uses, and more
r-wgcna
lcc
1.0
R package for Weighted Gene Co-expression Network Analysis (WGCNA), which is used for constructing co-expression networks and identifying modules of highly correlated genes.
R, Bioinformatics, Gene Expression, Network Analysis
Bioinformatics, Biological Sciences
Statistical Software
Documentation, Uses, and more
racon
mcc
1.0
Racon is consensus module for raw de novo DNA assembly of long uncorrected reads.
Bioinformatics, Sequence Analysis, Genomics
Genomics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
ragtag
lcc, mcc
1.0
Ragtag is a tool for fast reference-guided genome assembly scaffolding.
Assembly Improvement, Genome Alignment, Assembly Evaluation
Biological Sciences
Bioinformatics
Documentation, Uses, and more
raisd
mcc
1.0
Documentation, Uses, and more
randrproto
lcc
N/A
Documentation, Uses, and more
rapids
lcc
1.0
RAPIDS is a collection of open source software libraries and APIs that gives you the ability to execute end-to-end data science and analytics pipelines entirely on NVIDIA GPUs using familiar PyData APIs.
Description Source: https://rapids.ai/learn-more/#about
Data Science, Analytics, Gpu Computing
Computer Science, Computer & Information Sciences
Data Science
Documentation, Uses, and more
raxml
lcc, mcc
1.0
RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.
Description Source: https://github.com/amkozlov/raxml-ng
Phylogenetics, Evolutionary Biology, Bioinformatics
Systematics & Population Biology, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
raxml-ng
lcc
1.0
Raxml-ng is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.
Phylogenetics, Evolutionary Biology, Bioinformatics
Systematics & Population Biology, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
raxmlng
mcc
1.0
RAxML-NG is a software tool for maximum likelihood-based phylogenetic inference and ancestral state reconstruction.
phylogenetics, maximum likelihood, tree inference, bioinformatics
Bioinformatics, Biological Sciences
Executable
Documentation, Uses, and more
rcorrector
mcc
1.0
rcorrector is a software tool designed for correcting errors in RNA-Seq data, particularly useful for improving the accuracy of transcriptome assembly and quantification.
RNA-Seq, Error Correction, Bioinformatics, Transcriptomics
Bioinformatics, Biochemistry and Molecular Biology
Command-line tool
Documentation, Uses, and more
rdkit
lcc, mcc
1.0
RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
Description Source: https://github.com/rdkit/rdkit
Cheminformatics, Molecular Modeling, Cheminformatics Toolkit
Chemical Sciences, Natural Sciences
Toolkit
Documentation, Uses, and more
rdma-core
lcc, mcc
1.0
rdma-core is a set of userspace libraries and tools for Remote Direct Memory Access (RDMA) and kernel-level support for RDMA networking.
RDMA, Networking, High Performance Computing, InfiniBand
Computer Science
Library
Documentation, Uses, and more
rdma-core-devel
lcc, mcc
1.0
A set of libraries and daemons for Remote Direct Memory Access (RDMA) which enables high-throughput and low-latency networking.
Networking, High Performance Computing, RDMA
Networking, Computer Science
Library
Documentation, Uses, and more
re2c
ecc
N/A
re2c is a free and open-source lexer generator for C/C++, Go and Rust with a focus on generating fast code. It compiles regular expression specifications to deterministic finite automata and encodes them in the form of conditional jumps in the target language. This approach is generally faster than table-based lexers, and the generated code is easier to debug and understand.
Description Source: https://re2c.org/
Lexer, Scanner, Regular Expressions, Dfa
Software Engineering, Computer & Information Sciences
Tool
Documentation, Uses, and more
readline
ecc, lcc
1.0
The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
Gnu, Command Line Interface, Interactive Programs, Line Editing, History Manipulation
Software Engineering, Computer & Information Sciences
Command Line Tool
Documentation, Uses, and more
readline-devel
lcc, mcc
1.0
The readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The default editing mode is Emacs, but this can be changed when the application is run. In Emacs mode, the command line can be edited using the standard Emacs keystrokes.
Software Development, Library, Command Line Editing
Software Engineering, Engineering & Technology
Development
Documentation, Uses, and more
recon
mcc
1.0
Documentation, Uses, and more
reditools1
mcc
1.0
Documentation, Uses, and more
reditools2
mcc
1.0
Documentation, Uses, and more
reindeer
lcc
1.0
Documentation, Uses, and more
renderproto
lcc
N/A
Documentation, Uses, and more
repeatafterme
mcc
1.0
Documentation, Uses, and more
repeatmasker
mcc
1.0
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
Genomics, Bioinformatics, Sequence Analysis, Repeat Detection
Genetics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
repeatmodeler
mcc
1.0
RepeatModeler is a de novo transposable element (TE) family identification and modeling package.
Genomics, Bioinformatics, Repeat Sequences, De Novo Identification
Bioinformatics, Biological Sciences
Research Tool
Documentation, Uses, and more
repeatscout
mcc
1.0
RepeatScout is a tool to discover repetitive substrings in DNA.
Genomics, Bioinformatics, Computational Biology
Biological Sciences
Genomic Sequence Analysis
Documentation, Uses, and more
requests
ecc, lcc
1.0
Requests is a simple and elegant HTTP library for Python, built for human beings.
HTTP, API, Web Development, Python
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
requirements.txt
mcc
1.0
A file format used for specifying dependencies for Python projects, commonly used with pip.
Python, Dependency Management, Package Management
Software Engineering, Computer Science
Library
Documentation, Uses, and more
reshape2
lcc, mcc
1.0
reshape2 is an R package that provides functions to restructure and aggregate data, making it easier to manipulate and analyze datasets.
Data Manipulation, Data Reshaping, R Package
Statistics, Data Analysis
Library
Documentation, Uses, and more
reviewer
mcc
1.0
Documentation, Uses, and more
rmblast
mcc
1.0
rmblast is a high-performance implementation of the BLAST (Basic Local Alignment Search Tool) algorithm, optimized for rapid sequence alignment in bioinformatics applications.
bioinformatics, sequence alignment, BLAST, high-performance computing
Computational Biology, Biochemistry and Molecular Biology
Command-line tool
Documentation, Uses, and more
rnabloom
mcc
1.0
Documentation, Uses, and more
rnahybrid
mcc
1.0
RNAhybrid is a tool for predicting the hybridization of a single-stranded RNA to a target RNA or DNA sequence. It is particularly useful in the field of bioinformatics for studying RNA-RNA interactions.
bioinformatics, RNA, hybridization, computational biology
Bioinformatics, Molecular Biology
Command-line tool
Documentation, Uses, and more
rnammer
lcc
1.0
RNAmmer is a software tool for the annotation of ribosomal RNA genes in genomic sequences.
bioinformatics, genomics, RNA, annotation
Bioinformatics, Biological Sciences
Standalone
Documentation, Uses, and more
rnastructure
lcc
1.0
RNAstructure is a software package for RNA secondary structure prediction and analysis, providing tools for both thermodynamic and comparative methods.
RNA, Bioinformatics, Computational Biology, Molecular Biology
Bioinformatics, Biochemistry and Molecular Biology
Standalone
Documentation, Uses, and more
roary
lcc
1.0
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome.
Bioinformatics, Genomics, Pan-Genome Analysis, Prokaryotic Genomes
Genomics, Biological Sciences
Tool
Documentation, Uses, and more
root
lcc, mcc
1.0
ROOT is a framework for data processing, born at CERN, at the heart of the research on high-energy physics. Every day, thousands of physicists use ROOT applications to analyze their data or to perform simulations.
Description Source: https://root.cern/about/
Data Analysis, Visualization, High-Energy Physics, Data Manipulation, Statistical Analysis
Particle & High-Energy Physics, Physical Sciences
Library
Documentation, Uses, and more
rsem
mcc
1.0
RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation.
Description Source: https://github.com/deweylab/RSEM
RNA-Seq, Transcriptomics, Gene Expression, Bioinformatics
Genomics, Biological Sciences
Computational Tool
Documentation, Uses, and more
rstudio
lcc
1.0
RStudio is an integrated development environment (IDE) for the R and Python. It includes a console, syntax-highlighting editor that supports direct code execution, and tools for plotting, history, debugging and workspace management.
Description Source: https://posit.co/products/open-source/rstudio/
Ide, Statistical Computing, Data Visualization, Programming
Statistics, Other Natural Sciences
Ide
Documentation, Uses, and more
rsync
lcc, mcc
1.0
rsync is a fast and versatile file copying tool that can synchronize files and directories between two locations over a network or locally.
file transfer, synchronization, backup, networking
Computer Science
Command-line tool
Documentation, Uses, and more
rvtests
mcc
1.0
rvtests is a software package designed for the analysis of genetic association studies, particularly focusing on rare variants. It provides statistical methods to evaluate the association of rare variants with traits in a population.
genetics, bioinformatics, statistical analysis, rare variants
Bioinformatics, Genetics
Analysis Tool
Documentation, Uses, and more
rweka
lcc
1.0
rweka is an R package that provides a comprehensive framework for machine learning and data mining, offering a wide range of algorithms for classification, regression, clustering, and more.
Machine Learning, Data Mining, R Package, Weka
Computer Science, Artificial Intelligence and Intelligent Systems
Library
Documentation, Uses, and more
sabre
lcc
1.0
Documentation, Uses, and more
salmon
lcc, mcc
1.0
Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.
RNA-Seq, Transcript Expression Quantification
Genetics, Biological Sciences
Tool
Documentation, Uses, and more
salsa2
mcc
1.0
Documentation, Uses, and more
sambamba
mcc
1.0
Sambamba is a high performance highly parallel robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files.
Sam/Bam Files, High-Performance Tool, Parallel Processing, Genomics
Bioinformatics, Biological Sciences
Computational Software
Documentation, Uses, and more
samblaster
mcc
1.0
Samblaster is a tool to mark duplicates and extract discordant and split reads from sam files.
Bioinformatics, Hpc Tools
Bioinformatics, Biological Sciences
Analysis Tool
Documentation, Uses, and more
samtools
lcc, mcc
1.0
SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
Description Source: https://samtools.sourceforge.net/
Sequence Analysis, Genomics, Bioinformatics
Bioinformatics, Biological Sciences
Command Line Tool
Documentation, Uses, and more
samtools-bcftools-htslib
mcc
1.0
A suite of programs for interacting with high-throughput sequencing data, including tools for manipulating SAM/BAM/CRAM files and variant calling.
bioinformatics, genomics, data analysis, sequence alignment
Bioinformatics, Biological Sciences
Command-line tool
Documentation, Uses, and more
sbert
lcc
1.0
Documentation, Uses, and more
scalapack
lcc
N/A
The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
Linear-Algebra, Numerical-Computing, Distributed-Computing, Parallel-Computing
Other, Physical Sciences
Library
Documentation, Uses, and more
scalasca
lcc
N/A
Toolset for performance analysis of large-scale parallel applications
Performance Analysis, Parallel Applications, Performance Optimization, Mpi Applications, Visualization
Software Engineering, Systems & Development, Computer & Information Sciences
Performance Analysis Tool
Documentation, Uses, and more
scikit-learn
ecc, lcc
1.0
Scikit-learn is an open-source machine learning library for Python, known for its simplicity and accessibility. It provides a wide range of supervised and unsupervised learning algorithms, as well as tools for model fitting, data preprocessing, model selection, and evaluation.
Machine Learning, Python Library
Artificial Intelligence & Intelligent Systems, Computer & Information Sciences
Libraries
Documentation, Uses, and more
scipy
ecc, lcc, mcc
1.0
SciPy is a collection of mathematical algorithms and convenience functions built on NumPy . It adds significant power to Python by providing the user with high-level commands and classes for manipulating and visualizing data.
Description Source: https://docs.scipy.org/doc/scipy-1.8.0/tutorial/general.html
Scientific Computing, Numerical Algorithms, Python Library, Data Analysis, Signal Processing
Applied Mathematics, Computer & Information Sciences, Other Computer & Information Sciences
Python
Documentation, Uses, and more
scons
lcc
1.0
SCons is an Open Source software construction tool. Think of SCons as an improved, cross-platform substitute for the classic Make utility with integrated functionality similar to autoconf/automake and compiler caches such as ccache. In short, SCons is an easier, more reliable and faster way to build software.
Description Source: https://scons.org/
Build Tool, Software Construction, Automation, Python
Software Development, Engineering & Technology
Build Tool
Documentation, Uses, and more
scorep
lcc
N/A
Scalable Performance Measurement Infrastructure for Parallel Codes
Performance Analysis, Profiling, Tracing, HPC
Computer Science
Performance Analysis Tool
Documentation, Uses, and more
scotch
lcc
N/A
Graph, mesh and hypergraph partitioning library
Graph Partitioning, Mesh Partitioning, Parallel Computing, Distributed Memory
Software Engineering, Systems & Development, Computer & Information Sciences
Library
Documentation, Uses, and more
scte
mcc
1.0
Documentation, Uses, and more
sda
mcc
1.0
Documentation, Uses, and more
seaborn
ecc
1.0
Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. Description Source: https://github.com/conda-forge/seaborn-feedstock/blob/main/recipe/meta.yaml
Python Library, Data Visualization, Statistical Graphics
Statistics, Computer & Information Sciences
Library
Documentation, Uses, and more
sed
ecc
N/A
sed (Stream Editor) is a Unix utility that parses and transforms text from a data stream or file using a simple, compact programming language.
Text processing, Unix, Command line, Scripting
Software Engineering, Other Computer and Information Sciences
Command-line tool
Documentation, Uses, and more
sentence-transformers
lcc
1.0
Documentation, Uses, and more
seqkit
mcc
1.0
Seqkit is a rapid tool for manipulating fasta and fastq files.
Sequence Manipulation, Fasta, Fastq
Bioinformatics, Biological Sciences
Bioinformatics
Documentation, Uses, and more
seqsero2
lcc
1.0
Documentation, Uses, and more
seqtk
mcc
1.0
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It is designed for handling large sequence data efficiently.
bioinformatics, sequence processing, FASTA, FASTQ, data manipulation
Bioinformatics, Biological Sciences
Command-line tool
Documentation, Uses, and more
settarg
lcc, mcc
N/A
The settarg module works with Lmod to help developers manage their compiled software projects. It does so by making it easy to switch between optimized or debug builds; change compiler or other modules; and let the build system know about the changes. The secret of settarg is that it consolidates the state of a build into one environment variable called $TARG. \r
Description Source: https://lmod.readthedocs.io/en/latest/310_settarg.html
Compilers, Optimization, Performance Enhancement, Command-Line Tool
Command-Line Utility
Documentation, Uses, and more
setuptools
lcc
1.0
Easily download, build, install, upgrade, and uninstall Python packages
Python Packaging, Package Management, Dependency Management
Software Engineering, Computer Science
Library
Documentation, Uses, and more
shapeit.v2.r904.glibcv2.17.linux
mcc
1.0
SHAPEIT is a software tool for phasing genotype data, which is essential for various genetic analyses.
genomics, bioinformatics, phasing, genotype
Bioinformatics, Genomics
Command-line tool
Documentation, Uses, and more
shapeit2
mcc
1.0
shapeit2 is a software tool for phasing genotype data, which is essential for understanding the genetic architecture of traits and diseases.
Genetics, Bioinformatics, Phasing, Genotype
Bioinformatics, Genetics
Command-line tool
Documentation, Uses, and more
shapeit5
mcc
1.0
SHAPEIT5 is a software package to estimate haplotypes in large genotype datasets (WGS and SNP array).
Genomics, Data Phasing, Haplotype Inference
Genetics, Biological Sciences
Phasing Tool
Documentation, Uses, and more
shapely
mcc
1.0
Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.
Python Library, Geospatial Analysis, Geometric Objects
Geographic Information Science, Earth & Environmental Sciences
Python Library
Documentation, Uses, and more
sibeliaz
mcc
1.0
Sibelias is a software tool designed for the analysis of genomic sequences, particularly for detecting and visualizing genomic rearrangements and structural variations.
bioinformatics, genomics, structural variation, genomic analysis
Bioinformatics, Genomic Analysis
Analysis Tool
Documentation, Uses, and more
signalp
lcc, mcc
1.0
SignalP is a software tool for predicting the presence and location of signal peptide cleavage sites in amino acid sequences of proteins.
bioinformatics, protein prediction, signal peptides
Bioinformatics, Molecular Biology
Prediction Tool
Documentation, Uses, and more
sigprofilerextractor
lcc
1.0
SigProfilerExtractor is a software tool used for extracting mutational signatures from genomic data, particularly in the context of cancer genomics.
bioinformatics, cancer genomics, mutation analysis
Bioinformatics, Biochemistry and Molecular Biology
Command-line tool
Documentation, Uses, and more
singlem
mcc
1.0
SingleM is a tool for profiling shotgun metagenomes.
Microbial Genomics, Metagenomics, Genome Assembly, Variant Calling
Genomics, Biological Sciences
Bioinformatics
Documentation, Uses, and more
sionlib
lcc
N/A
Scalable I/O Library for Parallel Access to Task-Local Files
I/O Interface, Scientific Data, Hdf5 Files
High-Performance Computing, Computer Science
Library
Documentation, Uses, and more
slepc
lcc
N/A
A library for solving large scale sparse eigenvalue problems
Eigenvalue Problems, Sparse Matrices, Parallel Computing
Numerical Linear Algebra, Other Mathematics
Numerical Computing
Documentation, Uses, and more
slow5tools
mcc
1.0
slow5tools is a suite of tools for working with the slow5 file format, which is used for storing raw signal data from nanopore sequencing technologies.
bioinformatics, nanopore sequencing, data processing
Bioinformatics, Genomics
Command-line tools
Documentation, Uses, and more
snakemake
mcc
1.0
The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language.
Description Source: https://snakemake.readthedocs.io/en/stable/
Workflow Management, Reproducibility, Traceability, Bioinformatics, Computational Biology, Data Science
Bioinformatics, Other Computer & Information Sciences
Software
Documentation, Uses, and more
snap
lcc
1.0
Snap is a semi-HMM-based Nucleic Acid Parser -- gene prediction tool.
Network Analysis, Large Networks, Graph Algorithms
Computer Science, Computer & Information Sciences
Tool
Documentation, Uses, and more
snappy
lcc
N/A
Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.
Description Source: https://github.com/google/snappy
Compression, Big Data, Data Processing
Computer & Information Sciences
Data Processing Tool
Documentation, Uses, and more
sniffles
lcc, mcc
1.0
Sniffles is a tool for detecting and genotyping structural variants from long-read sequencing data.
genomics, bioinformatics, structural variants, long-read sequencing
Bioinformatics, Biochemistry and Molecular Biology
Command-line tool
Documentation, Uses, and more
sniffles-2.5.3
lcc
1.0
Sniffles is a tool for detecting structural variants in genomic data, specifically designed for analyzing long-read sequencing data.
Genomics, Bioinformatics, Structural Variants
Bioinformatics, Genomics
Command-line Tool
Documentation, Uses, and more
snippy
lcc
1.0
Snippy is a tool for rapid haploid variant calling and core genome alignment.
Haploid Variant Calling, Core Genome Alignments, Bacterial Isolates
Bioinformatics, Biological Sciences
Genomic Analysis Tool
Documentation, Uses, and more
snp-dists
lcc
1.0
Snp-dists is a tool to convert a FASTA alignment to SNP distance matrix.
Genomics, Bioinformatics, Sequence Analysis, Phylogenetics
Genomics, Biological Sciences
Analysis Tool
Documentation, Uses, and more
snp-sites
lcc
1.0
Snp-sites is a tool that apidly extracts SNPs from a multi-FASTA alignment.
Bioinformatics, Computational Biology, Genomics
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
soapdenovo
lcc
1.0
SOAPdenovo is a software package for de novo genome assembly from short reads, particularly designed for high-throughput sequencing data.
genome assembly, bioinformatics, high-throughput sequencing
Bioinformatics, Genomics
Open-source
Documentation, Uses, and more
soapdenovo2
lcc
1.0
Soapdenovo2 is a short-read assembly method to build de novo draft assembly.
De Novo Assembly, Short Reads, Illumina Platform
Bioinformatics, Biological Sciences
Bioinformatics
Documentation, Uses, and more
solote
mcc
1.0
Documentation, Uses, and more
sortedcontainers
mcc
1.0
SortedContainers is a Python library that provides sorted list, sorted dict, and sorted set data types. It is designed to be fast and efficient, with a focus on performance and ease of use.
Python, Data Structures, Sorting, Collections
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
sourmash
mcc
1.0
Sourmash is a tool for quickly search, compare, and analyze genomic and metagenomic data sets.
Bioinformatics, Genomics, Nucleotide Signatures, Minhash Sketches
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
spaceranger
mcc
1.0
Spaceranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images.
Bioinformatics, Hpc Tools
Molecular Biology, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
spack
ecc, lcc
N/A
Build and installation framework
Package Management, Software Installation, Dependency Management, Hpc, Scientific Computing
High Performance Computing, Other Computer & Information Sciences
Utility
Documentation, Uses, and more
spacy
ecc, lcc
1.0
spaCy is a free, open-source library for advanced Natural Language Processing (NLP) in Python.
Description Source: https://spacy.io/usage/spacy-101#whats-spacy
Nlp, Natural Language Processing, Python Library
Artificial Intelligence & Intelligent Systems, Computer & Information Sciences
Library
Documentation, Uses, and more
spades
lcc, mcc
1.0
SPAdes is a genome assembly software that is specifically designed for single-cell and multi-cell bacterial sequencing data. It uses a combination of de Bruijn graph algorithms and error correction methods to construct accurate genome sequences.
Genome Assembly, Bioinformatics, Computational Biology
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
splishsplash
lcc
1.0
SPlisHSPlasH is an open-source library for the physically-based simulation of fluids and solids. The simulation in this library is based on the Smoothed Particle Hydrodynamics (SPH) method which is a popular meshless Lagrangian approach to simulate complex fluid effects. The SPH formalism allows an efficient computation of a certain quantity of a fluid particle by considering only a finite set of neighboring particles. One of the most important research topics in the field of SPH methods is the simulation of incompressible fluids. SPlisHSPlasH implements current state-of-the-art pressure solvers (WCSPH, PCISPH, PBF, IISPH, DFSPH, PF) to simulate incompressibility. Moreover, the library provides different methods to simulate viscosity, surface tension, vorticity, elasticity, and drag forces.
Documentation, Uses, and more
sqanti3
lcc, mcc
1.0
SQANTI3 is a tool designed for the comprehensive assessment of transcriptome assemblies, particularly focusing on the quality and completeness of assembled transcripts.
bioinformatics, transcriptomics, RNA-seq, genomics
Bioinformatics, Transcriptomics
Analysis Tool
Documentation, Uses, and more
sqlite
ecc, lcc
N/A
SQLite is a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine.
Description Source: https://www.sqlite.org/
Relational Database, Sql, Database Management
Computer Science, Computer & Information Sciences
Library
Documentation, Uses, and more
sqlite-devel
lcc, mcc
1.0
Development files for SQLite, a C library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine.
Database, SQL, Embedded, C library
Software Engineering, Database Systems
Library
Documentation, Uses, and more
squashfs
ecc
N/A
SquashFS is a compressed read-only filesystem with built-in compression providing space-efficient storage. It is commonly used in embedded systems, live CDs, and Linux distributions to compress filesystem images and reduce storage space requirements while maintaining efficient access to files.
Filesystem, Compression, Read-Only
Computer Science, Computer & Information Sciences
Filesystem
Documentation, Uses, and more
squashfuse
ecc
N/A
Documentation, Uses, and more
squigualiser
mcc
1.0
Documentation, Uses, and more
sra-tools
lcc, mcc
1.0
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
Description Source: https://github.com/ncbi/sra-tools
Bioinformatics, Hpc Tools, Sequence Analysis, Data Processing, High-Throughput Sequencing
Bioinformatics, Biological Sciences
Analysis Tool
Documentation, Uses, and more
sshfs
ecc
N/A
SSHFS (SSH File System) is a filesystem client based on SSH (Secure Shell) that allows you to mount remote directories over a secure connection.
File System, SSH, Remote Access, Linux
Applied Computer Science, Computer Science
File System Client
Documentation, Uses, and more
stacks
lcc, mcc
1.0
Stacks is a software pipeline for building loci from RAD-seq
Software, Computational Biology, Bioinformatics
Genomics, Biological Sciences
Analysis Tool
Documentation, Uses, and more
star
lcc, mcc
1.0
STAR (Spliced Transcripts Alignment to a Reference) is a fast and highly accurate RNA sequencing read mapper. It aligns RNA-Seq reads to a reference genome or transcriptome, enabling comprehensive analysis of gene expression and alternative splicing.
Software, RNA-Seq, Read Aligner, Splice Junctions, Alternative Splicing
Genetics, Biological Sciences
Alignment Tool
Documentation, Uses, and more
starfish
mcc
1.0
Documentation, Uses, and more
stitch
mcc
1.0
Documentation, Uses, and more
stringr
lcc
1.0
stringr is a R package, part of the tidyverse, that provides a simple, consistent, and modern interface for working with character (text) data, making tasks like extracting, cleaning, and transforming strings much easier and more intuitive than base R functions.
R,string manipulation,data processing,text analysis
Data Science, Applied Computer Science
Library
Documentation, Uses, and more
stringtie
mcc
1.0
Stringtie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
RNA-Seq, Transcript Assembly, Transcript Quantification
Biological Sciences
Transcriptomics Tool
Documentation, Uses, and more
structure
lcc, mcc
1.0
Structure is a software package for using multi-locus genotype data to investigate population structure.
Population Genetics, Population Structure, Genotype Analysis, Data Analysis
Ecology, Biological Sciences
Analysis Tool
Documentation, Uses, and more
structure_threader
mcc
1.0
Documentation, Uses, and more
superlu
lcc
N/A
A general purpose library for the direct solution of linear equations
Linear Algebra, Sparse Matrix, Direct Solver, Computational Science
Applied Mathematics, Mathematics
Solver Library
Documentation, Uses, and more
superlu_dist
lcc
N/A
A general purpose library for the direct solution of linear equations
Linear Solver, Sparse Systems, Parallel Computing
Applied Mathematics, Mathematics
Library
Documentation, Uses, and more
svim-asm
lcc
1.0
Documentation, Uses, and more
svn
mcc
1.0
Subversion (svn) is a version control system that allows users to manage changes to files and directories over time. It is widely used for source code management in software development.
Version Control, Software Development, Collaboration, Source Code Management
Computer Science, Software Engineering
Version Control System
Documentation, Uses, and more
sweepfinder2
mcc
1.0
SweepFinder2 is a software tool designed to detect and analyze selective sweeps in genomic data, particularly in populations. It is an improvement over the original SweepFinder, providing enhanced performance and accuracy.
genomics, population genetics, bioinformatics, selective sweeps
Bioinformatics, Genomics
Analysis Tool
Documentation, Uses, and more
swig
lcc, mcc
1.0
SWIG (Simplified Wrapper and Interface Generator) is a software development tool for building scripting language interfaces to C and C++ programs. SWIG simplifies development by largely automating the task of scripting language integration--allowing developers and users to focus on more important problems. \r
Description Source: https://www.swig.org/Doc4.2/SWIGDocumentation.html
Software Development, Programming Tool, Scripting Languages, Interface Generator
Computer Science, Computer & Information Sciences, Software Engineering, Systems & Development
Interface Generator
Documentation, Uses, and more
syny
mcc
1.0
Documentation, Uses, and more
syri
mcc
1.0
Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.
Network Analysis, Visualization, Complex Networks
Computer & Information Sciences
Network Analysis Tool
Documentation, Uses, and more
sz
lcc
N/A
Documentation, Uses, and more
szip
lcc
N/A
Szip compression software, providing lossless compression of scientific data
Compression Tool, Scientific Data Sets, Hdf5 File Format
Computer Science
Utility
Documentation, Uses, and more
tabix
mcc
1.0
Tabix is a tool and file format for indexing and querying large tab-delimited text files like genomic variants in Variant Call Format (VCF). It enables fast retrieval of genomic intervals and regions from indexed files, allowing efficient access to specific data entries without loading entire files into memory.
Genomic Data, Indexing, Querying
Bioinformatics, Biological Sciences
Tool
Documentation, Uses, and more
talon
mcc
1.0
Talon is a Python package for identifying and quantifying known and novel genes/isoforms in long-read transcriptome data sets.
Long-Read RNA Sequencing, Transcript Isoform Analysis, Gene Expression Quantification
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
tama
lcc, mcc
1.0
Documentation, Uses, and more
tar
ecc, lcc, mcc
1.0
tar is a command-line utility used for archiving files and directories on Unix-based systems. It allows bundling multiple files and directories into a single archive file, often compressed using utilities like gzip or bzip2. tar is commonly used for backup, data transfer, and file compression tasks.
File Archiving, Compression, Terminal
Other, Computer & Information Sciences
File Management
Documentation, Uses, and more
tassel
lcc
1.0
TASSEL is a software package used to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
Bioinformatics, Genetic Analysis, Plant Biology
Genetics, Biological Sciences
Analysis Tool
Documentation, Uses, and more
tau
lcc
N/A
Tuning and Analysis Utilities Profiling Package
Software, Compiler, Hpc Tools
High-Performance Computing, Physical Sciences
Commercial
Documentation, Uses, and more
tbb
ecc, lcc
N/A
The Intel Threading Building Blocks (TBB) is a C++ library for parallel programming that enables developers to create multi-threaded applications efficiently. It offers high-level constructs for parallelism, task-based programming, and workload distribution, simplifying the development of scalable and performance-oriented applications.
Multicore Programming, Parallel Computing, C++ Library, High Performance Computing
Software Engineering, Computer & Information Sciences
Programming Library
Documentation, Uses, and more
tbb32
lcc
N/A
Intel Threading Building Blocks (TBB) is a widely used C++ template library developed by Intel for parallel programming on multi-core processors. TBB provides higher-level abstractions for parallelism, making it easier to write code that can take advantage of multicore processors.
Parallel Programming, Multi-Core Processors, C++ Template Library, Intel
Computer & Information Sciences
Library
Documentation, Uses, and more
tcl
ecc
N/A
Tcl (Tool Command Language) is a powerful dynamic programming language suitable for a wide range of uses, including web and desktop applications, networking, administration, and testing.
Description Source: https://www.tcl.tk/
Scripting Language, Dynamic Programming Language, Cross-Platform, Scripting
Software Engineering, Computer & Information Sciences
Language Interpreter
Documentation, Uses, and more
tcsh
lcc
1.0
Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.
Command-Line Interpreter, Shell Scripting, Unix-Like Operating Systems
Operating Systems, Computer & Information Sciences
Language Interpreter
Documentation, Uses, and more
tensorflow
ecc
1.0
TensorFlow is an open-source machine learning framework developed by the Google Brain team. It provides a comprehensive, flexible ecosystem of tools, libraries, and community resources that enables researchers and developers to build and deploy machine learning-powered applications easily.
Machine Learning, Deep Learning, Neural Networks, Model Training
Artificial Intelligence & Intelligent Systems, Computer & Information Sciences
Machine Learning Framework
Documentation, Uses, and more
tensorflow-gpu
lcc
1.0
TensorFlow is an open-source machine learning framework developed by Google, designed for both research and production environments. The GPU version leverages the power of graphics processing units to accelerate deep learning computations.
Machine Learning, Deep Learning, GPU Computing, Artificial Intelligence
Computer Science, Artificial Intelligence and Intelligent Systems
Framework
Documentation, Uses, and more
tess3r
mcc
1.0
Documentation, Uses, and more
tetools
lcc, mcc
1.0
Documentation, Uses, and more
texinfo
ecc, lcc
N/A
Texinfo is the official documentation format of the GNU project. It is used to create both online information and printed output from a single source.
Documentation, Markup Language, GNU, Open Source
Software Engineering, Other Computer and Information Sciences
Documentation Tool
Documentation, Uses, and more
texlive-base
lcc
1.0
TeX Live is a comprehensive distribution of TeX, LaTeX, and related programs and packages.
TeX, LaTeX, Typesetting, Document Preparation
Typesetting and Document Formatting, Other Natural Sciences
Typesetting System
Documentation, Uses, and more
texlive-cm-super
lcc
1.0
The cm-super package provides a set of high-quality fonts for TeX, including support for Cyrillic and other languages.
Fonts, TeX, LaTeX, Typesetting
Computer Science, Other Computer and Information Sciences
Font Package
Documentation, Uses, and more
texlive-collection-fontsrecommended
lcc
1.0
A collection of recommended fonts for TeX Live, providing a wide variety of font styles and types for typesetting documents.
TeX, Fonts, Typesetting, Document Preparation
Computer Science, Computer and Information Sciences
Font Collection
Documentation, Uses, and more
texlive-collection-latex
lcc
1.0
A collection of LaTeX packages and classes for typesetting documents in the TeX Live distribution.
LaTeX, Typesetting, Document Preparation
Computer Science, Computer and Information Sciences
Library
Documentation, Uses, and more
texlive-collection-latexrecommended
lcc
1.0
A collection of LaTeX packages that are recommended for most users, providing a comprehensive set of tools for typesetting documents.
LaTeX, Typesetting, Document Preparation, Scientific Writing
Typesetting, Computer Science
Collection
Documentation, Uses, and more
texlive-dvipng
lcc
1.0
dvipng is a utility that converts DVI (DeVice Independent) files to PNG (Portable Network Graphics) format, which is useful for displaying LaTeX documents on the web.
DVI, PNG, LaTeX, Document Conversion
Computer and Information Sciences, Other Computer and Information Sciences
Command Line Tool
Documentation, Uses, and more
texlive-latex
lcc
1.0
TeX Live is a comprehensive TeX document production system that includes LaTeX, a high-quality typesetting system. It is widely used for producing scientific and mathematical documents due to its powerful handling of formulas and bibliographies.
Typesetting, Document Preparation, Scientific Publishing, LaTeX
Computer Science
Typesetting System
Documentation, Uses, and more
texlive-type1cm
lcc
1.0
A package for LaTeX that provides Type 1 fonts for use in documents.
LaTeX, Fonts, Typesetting
Computer Science, Computer and Information Sciences
Font Package
Documentation, Uses, and more
tidyr
lcc
1.0
tidyr is an R package designed for data tidying, which is the process of transforming data into a format that is easy to work with for analysis and visualization.
Data Manipulation, Data Cleaning, R Package
Statistics, Data Analysis
Library
Documentation, Uses, and more
tidytext
lcc
1.0
A package for text mining and natural language processing in R, providing tools for transforming text data into tidy formats for analysis.
text mining, natural language processing, R, data science
Computer Science, Informatics
Library
Documentation, Uses, and more
time
lcc, mcc
1.0
The `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running.
Time, Measurement, Events, Synchronization
Other
Measurement & Timekeeping
Documentation, Uses, and more
tk
mcc
1.0
Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches.
Gui, Python, Toolkit, Desktop Applications
Software Engineering, Computer & Information Sciences, Computer Science, Systems & Development
Library
Documentation, Uses, and more
tk-devel
lcc
1.0
Documentation, Uses, and more
tm
lcc
1.0
Documentation, Uses, and more
tmhmm
lcc
1.0
TMHMM is a software tool for predicting transmembrane helices in proteins based on their amino acid sequences.
bioinformatics, protein structure, transmembrane prediction
Bioinformatics, Protein Structure Prediction
Prediction Tool
Documentation, Uses, and more
tokenizers
lcc
1.0
Tokenizers is a library for training and using tokenizers in natural language processing tasks. It provides a fast and efficient way to preprocess text data for machine learning models.
NLP, Tokenization, Machine Learning, Natural Language Processing
Artificial Intelligence, Natural Language Processing
Library
Documentation, Uses, and more
tools
lcc, mcc
1.0
Documentation, Uses, and more
tophat
lcc
1.0
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
RNA-Seq, Splice Junction Mapper, Genomics
Bioinformatics, Biological Sciences
Genomic Analysis Tool
Documentation, Uses, and more
topicmodels
lcc
1.0
topicmodels is an R package for fitting topic models, including Latent Dirichlet Allocation (LDA) and Correlated Topic Models (CTM). It provides tools for text mining and natural language processing.
Text Mining, Natural Language Processing, Machine Learning, Statistical Modeling
Computational Linguistics, Natural Language Processing
Library
Documentation, Uses, and more
torch
ecc
1.0
PyTorch is an open-source machine learning library based on the Torch library, used for applications such as natural language processing and computer vision.
Machine Learning, Deep Learning, Artificial Intelligence, Neural Networks, Computer Vision, Natural Language Processing
Computer Science, Artificial Intelligence and Intelligent Systems
Library
Documentation, Uses, and more
torch-geometric
lcc
1.0
A library for deep learning on irregular structures such as graphs and point clouds, built on top of PyTorch.
Graph Neural Networks, Deep Learning, Machine Learning, PyTorch
Computer Science, Artificial Intelligence and Intelligent Systems
Library
Documentation, Uses, and more
torchaudio
ecc
1.0
torchaudio is a library for audio processing in PyTorch, providing tools to work with audio data, including loading, transforming, and saving audio files.
Audio Processing, Deep Learning, Machine Learning, PyTorch
Machine Learning, Audio Processing
Library
Documentation, Uses, and more
torchmetrics
lcc
1.0
TorchMetrics is a collection of metrics for PyTorch that allows users to compute various metrics for model evaluation and performance tracking.
PyTorch, Machine Learning, Deep Learning, Metrics, Model Evaluation
Computer Science, Artificial Intelligence and Intelligent Systems
Library
Documentation, Uses, and more
torchvision
ecc
1.0
torchvision is a PyTorch library that provides computer vision utilities and pre-trained models for deep learning-based image processing tasks. It offers various tools for data loading, transformation, and model architecture specifically designed for computer vision applications.
Deep Learning, Computer Vision, Image Processing
Artificial Intelligence & Intelligent Systems, Computer & Information Sciences
Deep Learning
Documentation, Uses, and more
tpmcalculator
lcc, mcc
1.0
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files.
Bioinformatics, Computational Biology, RNA-Seq, Transcriptomics
Biological Sciences
Bioinformatics
Documentation, Uses, and more
tqdm
ecc, lcc
1.0
tqdm is a fast, extensible progress bar library for Python and command line applications. It provides a simple and customizable way to visualize the progress of iterative tasks, making it easier for users to track the execution of loops and tasks.
Progress Bar, Python, Data Visualization, Productivity Tool
Computer Science, Computer & Information Sciences
Package
Documentation, Uses, and more
trame
mcc
1.0
Trame is a framework for building interactive applications in Python, primarily aimed at scientific computing and visualization.
Python, Visualization, Scientific Computing, Web Applications
Computer Science
Framework
Documentation, Uses, and more
transdecoder
lcc
1.0
Transdecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
Bioinformatics, Computational Biology, Transcriptomics, Protein Prediction
Genetics, Biological Sciences
Tool
Documentation, Uses, and more
transformers
ecc, lcc
1.0
State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch Description Source: https://github.com/conda-forge/transformers-feedstock/blob/main/recipe/meta.yaml
Nlp, Deep Learning, Machine Learning
Artificial Intelligence & Intelligent Systems, Computer & Information Sciences
Machine Learning
Documentation, Uses, and more
transrate
lcc
1.0
Transrate is software for de-novo transcriptome assembly quality analysis.
Transcriptome Assembly, Quality Assessment, Bioinformatics
Genetics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
transrate-tools
lcc
1.0
Documentation, Uses, and more
travis
lcc
1.0
Documentation, Uses, and more
travis-src
lcc
1.0
Documentation, Uses, and more
trf
mcc
1.0
Documentation, Uses, and more
trilinos
lcc
N/A
A collection of libraries of numerical algorithms
Scientific Computing, Numerical Analysis, Parallel Computing, Computational Physics
Biology, Engineering & Technology
Library
Documentation, Uses, and more
trim-galore
lcc, mcc
1.0
Trim-galore is a wrapper tool that automates quality and adapter trimming to FastQ files.
Ngs Data Processing, Quality Control, Adapter Trimming
Bioinformatics, Biological Sciences
Data Processing Tool
Documentation, Uses, and more
trimmomatic
lcc, mcc
1.0
Trimmomatic is a widely-used tool in bioinformatics for the preprocessing and quality control of high-throughput sequencing data, such as those from next-generation sequencing platforms. It offers various functions to remove adapters, trim low-quality reads, and filter sequences based on user-defined parameters.
Ngs Data Processing, Quality Control, Bioinformatics
Biology, Biological Sciences
Tool
Documentation, Uses, and more
trinity
lcc, mcc
1.0
Trinity is a software tool used for de novo transcriptome assembly from RNA-Seq data. It is designed to reconstruct full-length transcripts and address the challenges of assembling transcriptomes without a reference genome, contributing to gene expression and functional analysis.
Bioinformatics, Computational Biology, Transcriptomics, RNA-Seq, De Novo Assembly
Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
trinityrnaseq
lcc
1.0
Trinity is a software package for de novo transcriptome assembly from RNA-Seq data. It is designed to reconstruct full-length transcripts from short reads, allowing for the analysis of gene expression and alternative splicing.
RNA-Seq, Transcriptome, Assembly, Bioinformatics
Bioinformatics, Biological Sciences
Assembly Tool
Documentation, Uses, and more
trnascan-se
lcc
1.0
tRNAscan-SE is a widely used software tool for the identification of transfer RNA (tRNA) genes in genomic sequences. It utilizes covariance models to predict tRNA structures and gene locations, providing valuable insights into tRNA biology and facilitating genomic annotation.
Bioinformatics, Genomics, Computational Biology, Sequence Analysis
Genomics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
trtools
mcc
1.0
TRTools includes a variety of utilities for filtering, quality control and analysis of tandem repeats downstream of genotyping them from next-generation sequencing.
Python Library, Data Transformation, Tabular Data, Data Manipulation
Computer & Information Sciences
Library
Documentation, Uses, and more
ttt
mcc
1.0
Documentation, Uses, and more
ucsc-bedgraphtobigwig
mcc
1.0
A tool for converting BEDGraph files to BigWig format, which is used for efficient visualization of genomic data.
genomics, bioinformatics, data visualization
Bioinformatics, Biological Sciences
Command-line tool
Documentation, Uses, and more
ucsc-liftover
mcc
1.0
UCSC LiftOver is a tool that facilitates the conversion of genomic coordinates between different assemblies of the same species or between different species.
Genomics, Bioinformatics, Coordinate Conversion
Computational Biology, Genomics
Command-line tool
Documentation, Uses, and more
ucsc_utils
mcc
1.0
Documentation, Uses, and more
ucx
ecc
N/A
UCX is a communication library implementing high-performance messaging
Communication Library, High-Performance Computing, Distributed Computing
Computer Science
Communication Library
Documentation, Uses, and more
udunits2-devel
mcc
1.0
A library for converting between different units of measurement.
units, measurement, conversion, library
Physical Sciences, Other Physical Sciences
Library
Documentation, Uses, and more
ukyaro427
lcc
1.0
Documentation, Uses, and more
ultra
mcc
1.0
Documentation, Uses, and more
ultra-bioinformatics
mcc
1.0
Documentation, Uses, and more
umf
ecc
N/A
Documentation, Uses, and more
uncalled4
mcc
1.0
Documentation, Uses, and more
unzip
ecc, lcc, mcc
1.0
UnZip is a utility tool used for extracting and viewing files compressed in the ZIP format. It allows users to decompress ZIP archives, extract individual files, and preserve the directory structure of the compressed content.
File Extraction, Compression, Utility
Computer Science, Computer & Information Sciences
File Extraction
Documentation, Uses, and more
util-linux
lcc
1.0
Set of Linux utilities
Linux, System Utilities, Command Line Tools
Operating Systems, Computer & Information Sciences
Operating System Tools
Documentation, Uses, and more
util-linux-uuid
ecc, lcc
N/A
util-linux-uuid is a command-line utility that allows users to generate universally unique identifiers (UUIDs) in various formats. UUIDs are 128-bit numbers used as identifiers for entities in computer systems with a high probability of being unique.
Uuid Generator, Command-Line Utility, Unique Identifier, Data Management
Computer Science, Computer & Information Sciences
Command-Line Tool
Documentation, Uses, and more
util-macros
lcc
N/A
util-macros is a collection of utility macros for C programmers to aid in simplifying common tasks and improving code readability. These macros are designed to enhance the efficiency and maintainability of C code by providing useful functions and utilities.
Programming, Development, C Programming, Utility Macros
Computer Science, Computer & Information Sciences
Utility
Documentation, Uses, and more
valgrind
lcc
N/A
Memory debugging utilities
Debugging, Profiling, Development Tool
Computer Science, Computer & Information Sciences
Programming Tool
Documentation, Uses, and more
vamb
mcc
1.0
VAMB (Variational Autoencoder for Metagenomic Bins) is a software tool designed for the binning of metagenomic contigs using variational autoencoders. It leverages deep learning techniques to improve the accuracy of binning in metagenomic studies.
bioinformatics, metagenomics, machine learning, deep learning, data analysis
Computational Biology, Bioinformatics
Open-source
Documentation, Uses, and more
variantbam
lcc
1.0
Documentation, Uses, and more
vcf2arlequindiploid
mcc
1.0
Documentation, Uses, and more
vcflib
lcc, mcc
1.0
vcflib is a C++ library for parsing and manipulating Variant Call Format (VCF) files, which are commonly used in bioinformatics for storing gene sequence variations.
bioinformatics, genomics, VCF, C++
Bioinformatics, Genomics
Library
Documentation, Uses, and more
vcftools
lcc, mcc
1.0
VCFtools is a versatile set of tools for working with Variant Call Format (VCF) files commonly used in genetics and genomics research. It allows researchers to perform various operations on genetic variation data, such as filtering, summarizing, and analyzing genetic variants in VCF format.
Genetic Variation Analysis, Variant Call Format (Vcf), Population Genetics, Bioinformatics
Bioinformatics, Biological Sciences
Data Analysis Tool
Documentation, Uses, and more
vclust
mcc
1.0
Documentation, Uses, and more
vcontact2
mcc
1.0
Documentation, Uses, and more
vcontact3
mcc
1.0
Documentation, Uses, and more
velocyto
lcc, mcc
1.0
A package for the analysis of expression dynamics in single cell RNA seq data. In particular, it enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols.
bioinformatics,single-cell RNA-seq,RNA velocity,data analysis
Molecular Biology, Biological Sciences
Analysis Tool
Documentation, Uses, and more
velocyto.py
mcc
1.0
Velocyto is a computational tool for the analysis of RNA velocity, which aims to estimate the future state of individual cells in single-cell RNA sequencing data. It provides algorithms for inferring the direction and rate of change in gene expression at the single-cell level, offering insights into cellular dynamics and differentiation.
Single-Cell RNA-Sequencing, RNA Velocity Analysis, Gene Expression Dynamics, Transcriptomic Analysis
Bioinformatics, Biological Sciences
Library
Documentation, Uses, and more
velvet
lcc, mcc
1.0
Velvet is a sequence assembler for very short reads.
Genomics, Bioinformatics, Sequencing, Assembly
Bioinformatics, Biological Sciences
Bioinformatics Tool
Documentation, Uses, and more
verifybamid2
mcc
1.0
Documentation, Uses, and more
verkko
mcc
1.0
Documentation, Uses, and more
verkko-2.2.1
mcc
1.0
Documentation, Uses, and more
vg
mcc
1.0
Variation graphs (vg) provides tools for working with genome variation graphs.
genomics, bioinformatics, variant analysis, graph theory
Bioinformatics, Genomics
Command Line Tool
Documentation, Uses, and more
vibrant
mcc
1.0
Documentation, Uses, and more
viennarna
lcc
1.0
Viennarna is a set of standalone programs and libraries used for prediction and analysis of RNA secondary structures.
RNA Secondary Structure, Bioinformatics, Computational Biology
Bioinformatics, Biological Sciences
Prediction & Analysis Tools
Documentation, Uses, and more
vim
lcc
1.0
Vim is a highly configurable text editor built to enable efficient text editing. It is an improved version of the vi editor distributed with most UNIX systems. Vim is often called a "programmer's editor," and so useful for programming that many consider it an entire IDE. It's not just for programmers, though. Vim is perfect for all kinds of text editing, from composing email to editing configuration files.
text editor,programming,open source,cross-platform
Software Development, Text Editing
Text Editor
Documentation, Uses, and more
vina
mcc
1.0
Vina is an open-source program for performing molecular docking, which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex.
molecular docking, bioinformatics, computational chemistry
Bioinformatics, Molecular Docking
Open-source
Documentation, Uses, and more
virsorter
mcc
1.0
VirSorter is a bioinformatics tool designed for the identification and annotation of viral sequences in metagenomic data. It employs a combination of sequence similarity and genomic features to detect viral sequences, making it a valuable resource for viromics studies.
bioinformatics, metagenomics, viral detection, sequence analysis
Genomics, Bioinformatics
Command-line tool
Documentation, Uses, and more
visit
lcc
N/A
Visit is an open-source, interactive parallel visualization and graphical analysis tool used for visualizing scientific data. It is particularly focused on large-scale simulations and post-processing of complex data sets, enabling researchers to analyze and present their data in a visually engaging manner.
Visualization, Data Analysis, Scientific Computing
Informatics, Analytics & Information Science, Computer & Information Sciences
Visualization Software
Documentation, Uses, and more
vpl
lcc
N/A
VPL (Virtual Programming Lab) is an online platform and learning environment for teaching and practicing programming concepts through interactive coding exercises and assignments. It provides a virtual environment where students can write, compile, and test code, allowing educators to create programming labs and assessments in various programming languages.
Visual Programming, Beginner-Friendly, Graphical Interface
Computer & Information Sciences
Language Programming
Documentation, Uses, and more
vtune
ecc, lcc
N/A
VTune Profiler, also known as Intel VTune, is a performance profiling tool developed by Intel. It enables developers to optimize software performance on Intel architecture platforms by providing detailed insights into application behavior, identifying performance bottlenecks, and suggesting optimizations.
Performance Optimization, Profiling, Intel Architecture
Software Engineering, Computer & Information Sciences
Profiling Tool
Documentation, Uses, and more
wandb
lcc
1.0
Weights & Biases (wandb) is a tool for tracking machine learning experiments, visualizing results, and collaborating on projects.
Machine Learning, Experiment Tracking, Data Visualization, Collaboration
Machine Learning, Artificial Intelligence and Intelligent Systems
Library
Documentation, Uses, and more
wget
ecc, lcc, mcc
1.0
GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.
Download Manager, Command-Line Tool
Computer Science, Computer & Information Sciences
System Tool
Documentation, Uses, and more
whatshap
mcc
1.0
Whatshap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.
Genomics, Bioinformatics, Variant Phasing
Bioinformatics, Biological Sciences
Tool
Documentation, Uses, and more
wheel
lcc
1.0
Wheel is a built-package format for Python that helps in the distribution of Python packages. It is designed to create a faster installation experience compared to traditional source distributions.
Python, Packaging, Distribution
Computer Science, Software Engineering
Packaging Tool
Documentation, Uses, and more
which
lcc, mcc
1.0
Documentation, Uses, and more
winnowmap
mcc
1.0
Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences.
Mapping, Alignment, Nanopore, Pacbio, Sequencing
Genetics, Biological Sciences
Sequence Alignment Tool
Documentation, Uses, and more
wrf-python
lcc
1.0
A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model.
Meteorology, Data Analysis, Visualization, Python, Scientific Computing
Meteorology, Weather Forecasting
Library
Documentation, Uses, and more
xcb-proto
lcc
N/A
Documentation, Uses, and more
xextproto
lcc
N/A
X11 Extension protocols and auxiliary headers
Linux, X11, X Window System
Computer & Information Sciences
Library
Documentation, Uses, and more
xlrd
ecc
1.0
xlrd is a library for reading data and formatting information from Excel files in the historical .xls format
excel parsing, data extraction, spreadsheet processing
Computational Data Analysis, Computer Science
Library
Documentation, Uses, and more
xorg-dev
lcc
1.0
xorg-dev is a package that provides development files for the X.Org X Window System, which is essential for building applications that utilize the X11 graphics system.
X Window System, Development, Linux, Graphics
Software Engineering, Computer Science
Development Library
Documentation, Uses, and more
xorg-macros
lcc
N/A
X.org macros utilities.
Build Tools, Autoconf Macros
Computer & Information Sciences
Library/Dependency
Documentation, Uses, and more
xproto
lcc
N/A
X protocol and ancillary headers
Software Development, Protocol Development, X Window System
Computer & Information Sciences
Library
Documentation, Uses, and more
xrandr
lcc
N/A
xrandr is a command-line tool for managing and configuring display settings in the X Window System. It allows users to set the size, orientation, and reflection of the outputs for the display.
Display Management, X Window System, Linux, Command Line Tool
Software Engineering, Other Computer and Information Sciences
Command Line Utility
Documentation, Uses, and more
xtea
mcc
1.0
Documentation, Uses, and more
xtrans
lcc
N/A
xtrans is a general-purpose transducer-based approach for defining translations between various formats and data representations. It provides a flexible framework for specifying bidirectional transformations between different data structures.
Data Transformation, Format Conversion, Transducer-Based Tool
Computer & Information Sciences
Tool
Documentation, Uses, and more
xvfb
mcc
1.0
Xvfb (X Virtual Frame Buffer) is a virtual X server that provides a virtual display framebuffer for running GUI applications without a physical display on Unix-like systems. It allows users to perform graphical operations in headless environments and is commonly used for automated testing and server-side applications.
Display Server, Headless, Virtual Display
Software Engineering, Computer & Information Sciences
Virtual Display Server
Documentation, Uses, and more
xz
ecc, lcc, mcc
1.0
xz: XZ utilities
Compression, Data Compression, Open-Source
Computer Science, Computer & Information Sciences
Utility
Documentation, Uses, and more
xz-devel
lcc, mcc
1.0
Development files for the XZ compression library, providing support for the LZMA and LZMA2 compression algorithms.
compression, decompression, data storage, file management
Computer Science, Applied Computer Science
Library
Documentation, Uses, and more
yahs
mcc
1.0
YaHS is a scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. YaHS has been tested in a wide range of genome assemblies.
Hi-C scaffolding, genome assembly, chromosome-scale assembly
Life Sciences, Bioinformatics
Documentation, Uses, and more
yak
mcc
1.0
Documentation, Uses, and more
ytorch
ecc
1.0
Documentation, Uses, and more
zfp
lcc
N/A
zfp is a compressed numerical array library providing high-throughput, low-overhead fixed-rate, fixed-precision encoding and compression of 1D and 2D scientific data.
Numerical Array, Compression, Scientific Data
Computer Science, Computer & Information Sciences
Library
Documentation, Uses, and more
zlib
lcc
N/A
zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.
Compression, Data Compression, File Compression, Deflate Algorithm
Software Engineering, Computer & Information Sciences
Data Compression
Documentation, Uses, and more
zlib-devel
lcc, mcc
1.0
zlib-devel is a development library for the zlib compression library, which provides in-memory compression and decompression functions.
compression, decompression, data processing, library
Computer Science
Library
Documentation, Uses, and more
zlib-ng
ecc
N/A
zlib-ng is a fast, efficient, and portable data compression library that is a drop-in replacement for zlib. It is designed to be compatible with zlib while providing improved performance and additional features.
compression, data processing, library, performance
Computer Science, Software Engineering
Library
Documentation, Uses, and more
zlib1g
lcc, mcc
1.0
zlib is a widely used data compression library that provides in-memory compression and decompression functions, including integrity checks, for use in various applications.
compression, decompression, data processing, library
Software Engineering, Other Computer and Information Sciences
Library
Documentation, Uses, and more
zlib1g-dev
lcc, mcc
1.0
zlib1g-dev is a development package for the zlib compression library, which provides functions for data compression and decompression.
compression, decompression, library, development
Computer Science, Software Engineering
Library
Documentation, Uses, and more
zstd
ecc, lcc
1.0
zstd (Zstandard) is a high-performance data compression library and command-line tool that offers fast compression and decompression speeds with the ability to achieve high compression ratios. It is designed to balance efficient compression and decompression with speed, making it suitable for various data processing and storage applications.
Compression, Data Compression, Algorithm
Computer Science, Computer & Information Sciences
Compression Algorithm
Documentation, Uses, and more
April 24, 2026 at 12:00:54 AM Eastern Daylight Time
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