BayesPeak protocols

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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

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Documentation


Publication for BayesPeak

BayesPeak in pipelines

 (3)
2016
PMCID: 4801952
PMID: 26903600
DOI: 10.15252/embj.201592532

[…] using multovl (aszodi, ) after identifying peaks with model‐based analysis of chip‐seq (macs) (zhang et al, )., 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. […]

2013
PMCID: 3608227
PMID: 23398888
DOI: 10.1186/1471-2164-14-92

[…] a cistrome analysis of jund between basal and two hour lps stimulated wky and wky.lcrgn2 bmdms using chip-seq (figure ). the aligned sequencing reads (additional file : table s2) were analysed using bayespeak [,] in order to identify areas of sequencing enrichment that signified jund-binding events, termed peaks. this analysis identified a greater number of peaks in wky basal and lps-stimulated […]

2013
PMCID: 3608227
PMID: 23398888
DOI: 10.1186/1471-2164-14-92

[…] tool v0.5.9 (bwa) []. read ends were trimmed if phred-scaled base quality scores dropped below 20. reads that uniquely mapped to the reference genome were used to detect areas of enrichment with bayespeak v1.1.3 [,] using a posterior probability threshold of 0.9. a stringent posterior probability threshold of 0.9 was used to filter all bins passing the threshold to form the final contiguous […]


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BayesPeak in publications

 (20)
PMCID: 5714215
PMID: 29036481
DOI: 10.1093/nar/gkx860

[…] 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 […]

PMCID: 5737333
PMID: 28605523
DOI: 10.1093/nar/gkx524

[…] was carried out using different algorithms and parameters to determine those returning the data that were more consistent with the distribution and location of sequencing reads. these were: macs (), bayespeak (), sicer (), homer () and t-pic (). based on the analysis of the results obtained (, , and ), we kept for further studies the collection of peaks returned by macs1.4 using (i) a cutoff […]

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

[…] statistics methods (intervalstats; chikina & troyanskaya, ). because the large brdu containing regions could not be identified by the macs peak calling algorithm, we identified these using the bayespeak algorithm (spyrou et al, ). for consistency, we re‐analyzed sororin chip‐seq data with the same algorithm, which identified 7,671 peaks in early s‐phase and 14,811 peaks in g2‐phase, […]

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 […]

PMCID: 4346620
PMID: 25695838
DOI: 10.1038/ncomms7329

[…] 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., macs-sorted cd4+ t cells described above were further purified as cd4+cd25–cd62l+cd44− naive t cells by facs, and cells were seeded at a density of 3 × 105 cells per 100 μl of rpmi […]


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

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