source("http://bioconductor.org/biocLite.R")
biocLite("CSAR")

CSAR

Statistical tools for the analysis of ChIP-seq data

Bioconductor version: 2.13

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:

source("http://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	1.14.0
In Bioconductor since	BioC 2.6 (R-2.11)
License	Artistic-2.0
Depends	R (>= 2.15.0), IRanges, GenomicRanges
Imports	stats, utils
Suggests	ShortRead, Biostrings
System Requirements
URL
Depends On Me
Imports Me	NarrowPeaks
Suggests Me	NarrowPeaks

Package Archives

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

Package Source	CSAR_1.14.0.tar.gz
Windows Binary	CSAR_1.14.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	CSAR_1.14.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats