BayesPeak

BayesPeak - an R package for analysing chip-seq data. Motivation: 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. Availability: Available as part of BioConductor version 2.6. URL: http://bioconductor.org/packages/release/bioc/html/BayesPeak.html

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References in zbMATH (referenced in 8 articles )

Showing results 1 to 8 of 8.
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  1. Benner, Philipp; Vingron, Martin: ModHMM: a modular supra-Bayesian genome segmentation method (2019)
  2. Alhaji, Baba B.; Dai, Hongsheng; Hayashi, Yoshiko; Vinciotti, Veronica; Harrison, Andrew; Lausen, Berthold: Bayesian analysis for mixtures of discrete distributions with a non-parametric component (2016)
  3. Ranciati, Saverio; Viroli, Cinzia; Wit, Ernst: Spatio-temporal model for multiple ChIP-seq experiments (2015)
  4. Rodríguez-Ezpeleta, Naiara (ed.); Hackenberg, Michael (ed.); Aransay, Ana M. (ed.): Bioinformatics for high throughput sequencing (2012)
  5. Cairns, Jonathan M.; Spyrou, Christiana; Stark, Rory; Smith, Mike L.; Lynch, Andy G.; Tavaré, Simon: Bayespeak - an R package for analysing chip-seq data (2011) ioport
  6. Humburg, Peter; Helliwell, Chris A.; Bulger, David; Stone, Glenn: Chipseqr: analysis of chip-seq experiments (2011) ioport
  7. Zhu, Lihua J.; Gazin, Claude; Lawson, Nathan D.; Pagès, Hervé; Lin, Simon M.; Lapointe, David S.; Green, Michael R.: Chippeakanno: a bioconductor package to annotate chip-seq and chip-chip data (2010) ioport
  8. Spyrou, Christiana; Stark, Rory; Lynch, Andy G.; Tavaré, Simon: Bayespeak: Bayesian analysis of chip-seq data (2009) ioport