CSAR

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see CSAR.

Statistical tools for the analysis of ChIP-seq data

Bioconductor version: 3.10

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 "3.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, Genetics, Software, Transcription
Version	1.38.0
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
System Requirements
URL

Suggests	ShortRead, Biostrings
Linking To
Enhances
Depends On Me
Imports Me	NarrowPeaks
Suggests Me	NarrowPeaks
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	CSAR_1.38.0.tar.gz
Windows Binary	CSAR_1.38.0.zip
Mac OS X 10.11 (El Capitan)	CSAR_1.38.0.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
Old Source Packages for BioC 3.10	Source Archive