ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

July 12, 2015
By

(This article was first published on R on G. Yu, and kindly contributed to R-bloggers)

My R/Bioconductor package,
ChIPseeker, published
in
Bioinformatics.

ChIPseeker had been
cited by http://www.biomedcentral.com/1471-2164/16/292 and
http://www.jbc.org/content/early/2015/06/18/jbc.M115.668558.short, and
was used (not cited) in
http://nar.oxfordjournals.org/content/early/2015/06/27/nar.gkv642.abstract
and
http://emboj.embopress.org/content/early/2014/12/18/embj.201490061.abstract.


ChIPseeker: an R/Bioconductor package for ChIP peak annotation,
comparison and visualization
G Yu, LG Wang, QY He.
Bioinformatics 2015, 31(14):2382-2383 DOI:
10.1093/bioinformatics/btv145

Summary: ChIPseeker is an R package for annotating ChIP-seq data
analysis. It supports annotating ChIP peaks and provides functions to
visualize ChIP peaks coverage over chromosomes and profiles of peaks
binding to TSS regions. Comparison of ChIP peak profiles and annotation
are also supported. Moreover, it supports evaluating significant overlap
among ChIP-seq datasets. Currently, ChIPseeker contains 15 000 bed file
information from GEO database. These datasets can be downloaded and
compare with user’s own data to explore significant overlap datasets for
inferring co-regulation or transcription factor complex for further
investigation. Availability and implementation: ChIPseeker is
released under Artistic-2.0 License. The source code and documents are
freely available through Bioconductor
(http://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html).

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