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W-ChIPeaks specifications


Unique identifier OMICS_07422
Name W-ChIPeaks
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Plants and Fungi
    • Arabidopsis thaliana
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus


  • person_outline Victor X. Jin

Publication for W-ChIPeaks

W-ChIPeaks citations


Identifying peaks in * seq data using shape information

BMC Bioinformatics
PMCID: 4905608
PMID: 27295177
DOI: 10.1186/s12859-016-1042-5

[…] have also been applied to this kind of signal. many statistical approaches such as poisson distributions (sissrs [], homer [], macs []), negative binomial distributions (zinba []), rank-statistics (w-chipeaks []), and cramér-von mises test (qeseq []) have been used. other approaches include clustering approach (sicer []), hidden markov models (chipdiff [], rseg []), tree shape statistics (tpic […]


Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP seq data

BMC Bioinformatics
PMCID: 3717085
PMID: 23721376
DOI: 10.1186/1471-2105-14-169

[…] procedures, in [] the normalization is performed only on commonly enriched regions. a control experiment is often used to aid the detection of truly enriched regions (e.g. in peakseq [] and w-chipeaks []). however, overall, there is a shortage of formal definition of chip efficiency and a limited focus on how this affects the interpretation of the results and how this should be fully […]


Genome wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2 mediated gene regulation

BMC Genomics
PMCID: 3599885
PMID: 23368971
DOI: 10.1186/1471-2164-14-70

[…] interacting regions, a publicly available [] chip-seq data of erα at the e2-treated and control condition in mcf7 cells was used. a total number of ~1,000 and ~12,047 peaks were called by using w-chipeaks [] in control and an e2 treated dataset, respectively. these peaks were used to examine the relationship between er occupancy and interaction frequency. the number of erα binding sites […]


Picking ChIP seq peak detectors for analyzing chromatin modification experiments

Nucleic Acids Res
PMCID: 3351193
PMID: 22307239
DOI: 10.1093/nar/gks048

[…] (), sicer () and sissrs (). for completeness, we added four algorithms to the comparative study that were not available when we designed the validation experiments: rseg (), swembl (), tpic () and w-chipeaks () (supplementary table s1a, b and supplementary notes a)., chip-seq datasets were analyzed with these 15 algorithms using the default or recommended settings. predicted events […]

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W-ChIPeaks institution(s)
Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA; Department of Informatics, University of Washington, Seattle, WA, USA
W-ChIPeaks funding source(s)
Supported by funds UL1RR025755 from the National Center for Research Resources, NIH, and from the Department of Biomedical Informatics, and the Ohio State University.

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