CSAR

Statistical tools for the analysis of ChIP-seq data

Bioconductor version: 2.8

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("CSAR")

Documentation

PDF R Script CSAR Vignette
PDF   Reference Manual

Details

biocViews ChIPseq, Transcription, Genetics
Depends R(>= 2.6.0)
Imports stats, utils
Suggests ShortRead, Biostrings
System Requirements
License Artistic-2.0
URL
Depends On Me
Imports Me
Suggests Me
Version 1.4.0
Since Bioconductor 2.6 (R-2.11)

Package Downloads

Package Source CSAR_1.4.0.tar.gz
Windows Binary CSAR_1.4.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary CSAR_1.4.0.tgz
Package Downloads Report Download Stats

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Fred Hutchinson Cancer Research Center