bPeaks (1.2)

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

http://cran.r-project.org/web/packages/bPeaks

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.

Maintainer: Gaelle LELANDAIS
Author(s): Jawad MERHEJ and Gaelle LELANDAIS

License: GPL

Uses: Does not use any package

Released almost 6 years ago.


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