Bioconductor - sarks

Bioconductor - sarks
Bioconductor 3.22
Software Packages
sarks
sarks
This is the
released
version of sarks; for the devel version, see
sarks
Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains
DOI:
10.18129/B9.bioc.sarks
Bioconductor version:
Release (3.22)
Suffix Array Kernel Smoothing (see https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797), or SArKS, identifies sequence motifs whose presence correlates with numeric scores (such as differential expression statistics) assigned to the sequences (such as gene promoters). SArKS smooths over sequence similarity, quantified by location within a suffix array based on the full set of input sequences. A second round of smoothing over spatial proximity within sequences reveals multi-motif domains. Discovered motifs can then be merged or extended based on adjacency within MMDs. False positive rates are estimated and controlled by permutation testing.
Author:
Dennis Wylie [aut, cre]
ORCID: 0000-0003-0380-3549
Maintainer:
Dennis Wylie
Citation (from within R, enter
citation("sarks")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("sarks")
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("sarks")
sarks-vignette
PDF
R Script
Reference Manual
PDF
NEWS
Text
LICENSE
Text
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Details
biocViews
DifferentialExpression
FeatureExtraction
GeneExpression
GeneRegulation
MotifDiscovery
RNASeq
Software
Transcriptomics
Version
1.22.0
In Bioconductor since
BioC 3.11 (R-4.0) (6 years)
License
BSD_3_clause + file
LICENSE
Depends
R (>= 4.0)
Imports
rJava
Biostrings
IRanges
, utils, stats,
cluster
binom
System Requirements
Java (>= 1.8)
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Source Package
sarks_1.22.0.tar.gz
Windows Binary (x86_64)
sarks_1.22.0.zip
macOS Binary (x86_64)
sarks_1.22.0.tgz
macOS Binary (arm64)
sarks_1.22.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/sarks
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/sarks
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