bPeaks: bPeaks: an intuitive peak-calling strategy to detect transcription factor binding sites from ChIP-seq data in small eukaryotic genomes

bPeaks is a simple approach to identify transcription factor binding sites from ChIP-seq data. Our general philosophy is to provide an easy-to-use tool, well-adapted for small eukaryotic genomes (< 20 Mb). bPeaks uses a combination of 4 cutoffs (T1, T2, T3 and T4) to mimic "good peak" properties as described by biologists who visually inspect the ChIP-seq data on a genome browser. For yeast genomes, bPeaks calculates the proportion of peaks that fall in promoter sequences. These peaks are good candidates as transcription factor binding sites.

Version: 1.2
Depends: R (≥ 2.10)
Published: 2014-02-28
Author: Jawad MERHEJ and Gaelle LELANDAIS
Maintainer: Gaelle LELANDAIS <gaelle.lelandais at univ-paris-diderot.fr>
License: GPL-2 | GPL-3 [expanded from: GPL]
NeedsCompilation: no
CRAN checks: bPeaks results

Downloads:

Reference manual: bPeaks.pdf
Package source: bPeaks_1.2.tar.gz
Windows binaries: r-devel: bPeaks_1.2.zip, r-release: bPeaks_1.2.zip, r-oldrel: bPeaks_1.2.zip
OS X Mavericks binaries: r-release: bPeaks_1.2.tgz, r-oldrel: bPeaks_1.2.tgz
Old sources: bPeaks archive

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