Bioconductor - gCrisprTools

Bioconductor - gCrisprTools
Bioconductor 3.22
Software Packages
gCrisprTools
gCrisprTools
This is the
released
version of gCrisprTools; for the devel version, see
gCrisprTools
Suite of Functions for Pooled Crispr Screen QC and Analysis
DOI:
10.18129/B9.bioc.gCrisprTools
Bioconductor version:
Release (3.22)
Set of tools for evaluating pooled high-throughput screening experiments, typically employing CRISPR/Cas9 or shRNA expression cassettes. Contains methods for interrogating library and cassette behavior within an experiment, identifying differentially abundant cassettes, aggregating signals to identify candidate targets for empirical validation, hypothesis testing, and comprehensive reporting. Version 2.0 extends these applications to include a variety of tools for contextualizing and integrating signals across many experiments, incorporates extended signal enrichment methodologies via the "sparrow" package, and streamlines many formal requirements to aid in interpretablity.
Author:
Russell Bainer, Dariusz Ratman, Steve Lianoglou, Peter Haverty
Maintainer:
Russell Bainer
Citation (from within R, enter
citation("gCrisprTools")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("gCrisprTools")
For older versions of R, please refer to the appropriate
Bioconductor release
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("gCrisprTools")
Contrast_Comparisons_gCrisprTools
HTML
R Script
Example_Workflow_gCrisprTools
HTML
R Script
gCrisprTools_Vignette
HTML
R Script
Reference Manual
PDF
NEWS
Text
Need some help? Ask on the Bioconductor Support site!
Details
biocViews
BiomedicalInformatics
CRISPR
CellBiology
DifferentialExpression
ExperimentalDesign
FunctionalGenomics
GeneSetEnrichment
Genetics
ImmunoOncology
MultipleComparison
Normalization
Pharmacogenetics
Pharmacogenomics
PooledScreens
Preprocessing
QualityControl
RNASeq
Regression
Software
SystemsBiology
Visualization
Version
2.16.0
In Bioconductor since
BioC 3.4 (R-3.3) (9.5 years)
License
Artistic-2.0
Depends
R (>= 4.1)
Imports
Biobase
limma
RobustRankAggreg
ggplot2
SummarizedExperiment
, grid,
rmarkdown
, grDevices, graphics, methods,
ComplexHeatmap
, stats, utils, parallel
System Requirements
URL
See More
Suggests
edgeR
knitr
AnnotationDbi
org.Mm.eg.db
org.Hs.eg.db
BiocGenerics
markdown
RUnit
sparrow
msigdbr
fgsea
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report
Build Report
Package Archives
Follow
Installation
instructions to use this package in your R session.
Source Package
gCrisprTools_2.16.0.tar.gz
Windows Binary (x86_64)
gCrisprTools_2.16.0.zip
macOS Binary (x86_64)
gCrisprTools_2.16.0.tgz
macOS Binary (arm64)
gCrisprTools_2.16.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/gCrisprTools
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/gCrisprTools
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