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

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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.

Author
Jawad MERHEJ and Gaelle LELANDAIS
Date of publication
2014-02-28 17:55:13
Maintainer
Gaelle LELANDAIS <gaelle.lelandais@univ-paris-diderot.fr>
License
GPL
Version
1.2

View on CRAN

Man pages

baseLineCalc
Function to calculate the average number of reads mapped on...
bPeaksAnalysis
Function to run the entire bPeaks procedure
bPeaks-package
bPeaks: an intuitive peak-calling strategy to detect...
dataPDR1
ChIP-seq results (IP and control samples) obtained with the...
dataReading
Function to import sequencing results in R
dataSmoothing
Function to smooth sequencing coverage along a chromosome
peakDetection
Peak calling method, i. e. identification of genomic regions...
peakDrawing
Function to draw graphical representations of genomic regions...
peakLocation
Function to locate detected basic peaks (bPeaks) according to...
yeastCDS
Annotations of CDS for different yeast species

Files in this package

bPeaks
bPeaks/NAMESPACE
bPeaks/data
bPeaks/data/yeastCDS.rda
bPeaks/data/dataPDR1.rda
bPeaks/data/datalist
bPeaks/R
bPeaks/R/bPeaksAnalysis.R
bPeaks/R/peakDetection.R
bPeaks/R/baseLineCalc.R
bPeaks/R/peakDrawing.R
bPeaks/R/dataSmoothing.R
bPeaks/R/dataReading.R
bPeaks/R/peakLocation.R
bPeaks/MD5
bPeaks/DESCRIPTION
bPeaks/man
bPeaks/man/dataReading.Rd
bPeaks/man/peakDetection.Rd
bPeaks/man/peakLocation.Rd
bPeaks/man/bPeaks-package.Rd
bPeaks/man/dataSmoothing.Rd
bPeaks/man/peakDrawing.Rd
bPeaks/man/baseLineCalc.Rd
bPeaks/man/yeastCDS.Rd
bPeaks/man/dataPDR1.Rd
bPeaks/man/bPeaksAnalysis.Rd