DOI: 10.18129/B9.bioc.CSAR    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see CSAR.

Statistical tools for the analysis of ChIP-seq data

Bioconductor version: 3.7

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 <jose.muino at live.com>

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PDF R Script CSAR Vignette
PDF   Reference Manual


biocViews ChIPSeq, Genetics, Software, Transcription
Version 1.32.0
In Bioconductor since BioC 2.6 (R-2.11) (8.5 years)
License Artistic-2.0
Depends R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
Imports stats, utils
Suggests ShortRead, Biostrings
Depends On Me
Imports Me NarrowPeaks
Suggests Me NarrowPeaks
Links To Me
Build Report  

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Source Package CSAR_1.32.0.tar.gz
Windows Binary CSAR_1.32.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) CSAR_1.32.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CSAR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CSAR
Package Short Url http://bioconductor.org/packages/CSAR/
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