ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
Version 3.12.4

The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs). This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages.

Package details

AuthorLihua Julie Zhu, Jianhong Ou, Jun Yu, Herve Pages, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe and Michael Green
Bioconductor views Annotation ChIPSeq ChIPchip
MaintainerLihua Julie Zhu <[email protected]>, Jianhong Ou <[email protected]>
LicenseGPL (>= 2)
Package repositoryView on Bioconductor
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ChIPpeakAnno documentation built on Dec. 8, 2017, 2:01 a.m.