CSAR

Statistical tools for the analysis of ChIP-seq data

Bioconductor version: Development (3.0)

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, Genetics, Software, Transcription
Version 1.17.0
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 Downloads

Package Source CSAR_1.17.0.tar.gz
Windows Binary CSAR_1.17.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) CSAR_1.17.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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