{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T04:22:15Z","timestamp":1777522935603,"version":"3.51.4"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,10,6]],"date-time":"2016-10-06T00:00:00Z","timestamp":1475712000000},"content-version":"vor","delay-in-days":2089,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: Available as part of BioConductor version 2.6. URL: http:\/\/bioconductor.org\/packages\/release\/bioc\/html\/BayesPeak.html<\/jats:p>\n               <jats:p>Contact: \u00a0jonathan.cairns@cancer.org.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq685","type":"journal-article","created":{"date-parts":[[2011,1,19]],"date-time":"2011-01-19T01:29:49Z","timestamp":1295400589000},"page":"713-714","source":"Crossref","is-referenced-by-count":38,"title":["BayesPeak\u2014an R package for analysing ChIP-seq data"],"prefix":"10.1093","volume":"27","author":[{"given":"Jonathan","family":"Cairns","sequence":"first","affiliation":[{"name":"1 Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, 2MRC Clinical Sciences Centre, Imperial College, Faculty of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN and 3Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christiana","family":"Spyrou","sequence":"additional","affiliation":[{"name":"1 Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, 2MRC Clinical Sciences Centre, Imperial College, Faculty of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN and 3Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rory","family":"Stark","sequence":"additional","affiliation":[{"name":"1 Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, 2MRC Clinical Sciences Centre, Imperial College, Faculty of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN and 3Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mike L.","family":"Smith","sequence":"additional","affiliation":[{"name":"1 Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, 2MRC Clinical Sciences Centre, Imperial College, Faculty of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN and 3Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andy G.","family":"Lynch","sequence":"additional","affiliation":[{"name":"1 Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, 2MRC Clinical Sciences Centre, Imperial College, Faculty of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN and 3Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, 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