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bPeaks (version 1.0)

bPeaks: a simple and intuitive approach for detection of basic peaks (bPeaks) from ChIP-seq data

Description

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. Instead of complex statistical models, bPeaks uses a combination of 4 cutoffs to mimic "good peak" properties as described by biologists who visually inspect the ChIP-seq data on a genome browser.

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Version

Install

install.packages('bPeaks')

Monthly Downloads

18

Version

1.0

License

GPL

Maintainer

Gaelle LELANDAIS

Last Published

April 2nd, 2013

Functions in bPeaks (1.0)

baseLineCalc

Function to calculate the average number of reads mapped on each nucleotide in a genome
bPeaksAnalysis

Function to run the entire bPeaks procedure
peakDrawing

Function to draw graphical representations of genomic regions detected using bPeaks methodology
dataSmoothing

Function to smooth sequencing coverage along a chromosome
dataReading

Function to import sequencing results in R
dataPDR1

ChIP-seq results (IP and control samples) obtained with the transcription factor Pdr1 in yeast Saccharomyces cerevisiae
peakDetection

Peak calling method, i. e. identification of genomic regions with a high density of sequences (reads)
bPeaks-package

bPeaks: a simple and intuitive approach for detection of basic peaks (bPeaks) from ChIP-seq data
peakLocation

Function to locate detected basic peaks (bPeaks) according to predifined chromosomal features