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CSAR

Statistical tools for the analysis of ChIP-seq data


Bioconductor version: Release (3.18)

Statistical tools for ChIP-seq data analysis. The package includes the statistical method described in Kaufmann et al. (2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation.

Author: Jose M Muino

Maintainer: Jose M Muino <jose.muino at live.com>

Citation (from within R, enter citation("CSAR")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CSAR")

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("CSAR")
CSAR Vignette PDF R Script
Reference Manual PDF

Details

biocViews ChIPSeq, Genetics, Software, Transcription
Version 1.54.0
In Bioconductor since BioC 2.6 (R-2.11) (14 years)
License Artistic-2.0
Depends R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
Imports stats, utils
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Suggests ShortRead, Biostrings
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CSAR_1.54.0.tar.gz
Windows Binary CSAR_1.54.0.zip
macOS Binary (x86_64) CSAR_1.54.0.tgz
macOS Binary (arm64) CSAR_1.54.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CSAR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CSAR
Bioc Package Browser https://code.bioconductor.org/browse/CSAR/
Package Short Url https://bioconductor.org/packages/CSAR/
Package Downloads Report Download Stats