To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

CSAR

Statistical tools for the analysis of ChIP-seq data

Bioconductor version: Release (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>

Citation (from within R, enter citation("CSAR")):

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 1.18.0
In Bioconductor since BioC 2.6 (R-2.11)
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.

Package Source CSAR_1.18.0.tar.gz
Windows Binary CSAR_1.18.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) CSAR_1.18.0.tgz
Mac OS X 10.9 (Mavericks) CSAR_1.18.0.tgz
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