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BayesPeak specifications

Information


Unique identifier OMICS_00432
Name BayesPeak
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.12.0
Stability Stable
Requirements
graphics, IRanges, R(>=2.14)
Maintained Yes

Versioning


No version available

Documentation


Publications for BayesPeak

BayesPeak citations

 (22)
call_split

Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803

2017
Nucleic Acids Res
PMCID: 5714215
PMID: 29036481
DOI: 10.1093/nar/gkx860
call_split See protocol

[…] normalized for visual inspection in the Integrative Genomics Viewer (IGV) (), using BamCoverage from DeepTools2 (). Peaks for NtcA were identified by two peak calling algorithms: MACS (v1.4.1) () and BayesPeaK (v1.22.0) (). In both algorithms, the background noise of unspecific binding was modeled using the input data (control DNA). Surrounding genes were retrieved using the Bioconductor package C […]

library_books

Retrotransposons are specified as DNA replication origins in the gene poor regions of Arabidopsis heterochromatin

2017
Nucleic Acids Res
PMCID: 5737333
PMID: 28605523
DOI: 10.1093/nar/gkx524

[…] ome size (,,). The total number of ORIs retrieved in each case was different, with SICER and T-PICs returning the largest values. A pair-wise comparison between different algorithms showed that MACS, BayesPeak and Homer rendered quite similar results as revealed by the percentage of coincidence (Supplememtary Figure S2C). Finally, visual inspection of the original reads in the genome browser acros […]

library_books

Recent advances in ChIP seq analysis: from quality management to whole genome annotation

2016
Brief Bioinform
PMCID: 5444249
PMID: 26979602
DOI: 10.1093/bib/bbw023

[…] Poisson model is typically experimentally observed, and the negative binomial model that is an extension of the Poisson model was adopted to approximate such an overdispersion (e.g. CisGenome [] and BayesPeak []). This model was extended to a zero-inflated negative binomial model to account for the zero-inflated read distribution caused by a lack of sequencing depth and low-mappable regions (e.g. […]

library_books

Sororin actively maintains sister chromatid cohesion

2016
PMCID: 4801952
PMID: 26903600
DOI: 10.15252/embj.201592532

[…] BrdU‐positive genomic regions and sororin peaks were called using the R package BayesPeak (Spyrou et al, ) version 1.18.2, with 1,000 bp bin size and corresponding control samples. Enriched bins were filtering for posterior probability > 0.5 and adjacent bins merged. Dependence o […]

library_books

Mediator independently orchestrates multiple steps of preinitiation complex assembly in vivo

2015
Nucleic Acids Res
PMCID: 4627066
PMID: 26240385
DOI: 10.1093/nar/gkv782

[…] PeakAnalyzer software for the subdivision of ChIP-seq regions into discrete peaks (). The significantly enriched regions were also identified in the control ChIP sample with an untagged strain using Bayespeak version 1.10.0 () with a threshold of 0.9. Around 200 peaks were identified by this method in the control sample and they were used to correct peakcalling data from Med15, Rad3, Kin28 and TB […]

call_split

TGF β3 expressing CD4+CD25−LAG3+ regulatory T cells control humoral immune responses

2015
Nat Commun
PMCID: 4346620
PMID: 25695838
DOI: 10.1038/ncomms7329
call_split See protocol

[…] of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. Krox20 peak locations were determined using the Bioconductor package BayesPeak. […]

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BayesPeak institution(s)
Department of Oncology, University of Cambridge, Li Ka Shing Centre, Cambridge, UK

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