CSAR

DOI: 10.18129/B9.bioc.CSAR    

Statistical tools for the analysis of ChIP-seq data

Bioconductor version: Release (3.6)

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 wur.nl>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CSAR")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CSAR")

 

PDF	R Script	CSAR Vignette
PDF		Reference Manual

Details

biocViews	ChIPSeq, Genetics, Software, Transcription
Version	1.30.0
In Bioconductor since	BioC 2.6 (R-2.11) (8 years)
License	Artistic-2.0
Depends	R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
Imports	stats, utils
LinkingTo
Suggests	ShortRead, Biostrings
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	NarrowPeaks
Suggests Me	NarrowPeaks
Build Report

Package Archives

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

Source Package	CSAR_1.30.0.tar.gz
Windows Binary	CSAR_1.30.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	CSAR_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CSAR
Package Short Url	http://bioconductor.org/packages/CSAR/
Package Downloads Report	Download Stats