BayesPeak--an R package for analysing ChIP-seq data.
BACKGROUND
Identification of genomic regions of interest in ChIP-seq data, commonly referred to as peak-calling, aims to find the locations of transcription factor binding sites, modified histones or nucleosomes. The BayesPeak algorithm was developed to model the data structure using Bayesian statistical techniques and was shown to be a reliable method, but did not have a full-genome implementation.


RESULTS
In this note we present BayesPeak, an R package for genome-wide peak-calling that provides a flexible implementation of the BayesPeak algorithm and is compatible with downstream BioConductor packages. The BayesPeak package introduces a new method for summarizing posterior probability output, along with methods for handling overfitting and support for parallel processing. We briefly compare the package with other common peak-callers.


BACKGROUND
Available as part of BioConductor version 2.6. URL: http://bioconductor.org/packages/release/bioc/html/BayesPeak.html.
Department of Oncology, University of Cambridge, Li Ka Shing Centre, Cambridge, UK. jonathan.cairns@cancer.org.uk
Jonathan
J
Cairns
Christiana
C
Spyrou
Rory
R
Stark
Mike L
ML
Smith
Andy G
AG
Lynch
Simon
S
Tavaré
D000465:Algorithms; D001499:Bayes Theorem; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D016678:Genome; D008390:Markov Chains; D051603:Recoverin; D012984:Software
D051603:Recoverin
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