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

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...

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Bibliographic Details
Published in:Bioinformatics 2015-07, Vol.31 (14), p.2382-2383
Main Authors: Yu, Guangchuang, Wang, Li-Gen, He, Qing-Yu
Format: Article
Language:English
Subjects:
Annotations
Binding Sites
Bioinformatics
Chips
Chromatin Immunoprecipitation
Computer Graphics
Data processing
DNA - chemistry
DNA - metabolism
High-Throughput Nucleotide Sequencing
HTML
Licenses
Molecular Sequence Annotation
Packages
Sequence Analysis, DNA
Software
Transcription Factors - metabolism
Transcription Initiation Site
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Description
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. 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).
ISSN:1367-4803
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btv145