CSAR

Statistical tools for the analysis of ChIP-seq data

Bioconductor version: Release (2.7)

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

To install this package, start R and enter:

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

Documentation

PDF

R Script

CSAR Vignette

Reference Manual

Details

biocViews	ChIPseq, Transcription, Genetics
Depends	R
Imports	stats, utils
Suggests	ShortRead, Biostrings
System Requirements
License	Artistic-2.0
URL
Depends On Me
Imports Me
Suggests Me
Version	1.2.0

Package Downloads

Package Source	CSAR_1.2.0.tar.gz
Windows Binary	CSAR_1.2.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	CSAR_1.2.0.tgz
Package Downloads Report	Download Stats