Introduction

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.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.Available as part of BioConductor version 2.6. URL: http://bioconductor.org/packages/release/bioc/html/BayesPeak.html.

Publications

  1. BayesPeak--an R package for analysing ChIP-seq data.
    Cite this
    Cairns J, Spyrou C, Stark R, Smith ML, Lynch AG, Tavaré S, 2011-03-01 - Bioinformatics (Oxford, England)

Credits

  1. Jonathan Cairns
    Developer

    Department of Oncology, University of Cambridge

  2. Christiana Spyrou
    Developer

  3. Rory Stark
    Developer

  4. Mike L Smith
    Developer

  5. Andy G Lynch
    Developer

  6. Simon Tavaré
    Investigator

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Summary
AccessionBT000156
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted BySimon Tavaré