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ChIPpeakAnno

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Facilitates batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions. The binding sites annotated with ChIPpeakAnno can be viewed easily as a table, a pie chart or plotted in histogram form, i.e., the distribution of distances to the nearest genes for each set of peaks. ChIPpeakAnno also offers functionalities for determining the significance of overlap between replicates or binding sites among transcription factors within a complex, and for drawing Venn diagrams to visualize the extent of the overlap between replicates. Furthermore, it includes functionalities to retrieve sequences flanking putative binding sites for PCR amplification, cloning, or motif discovery, and to identify Gene Ontology (GO) terms associated with adjacent genes.

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ChIPpeakAnno classification

ChIPpeakAnno specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Stability:
Stable

ChIPpeakAnno distribution

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No versioning.

ChIPpeakAnno support

Documentation

Credits

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Publications

Institution(s)

Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA

Link to literature

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