LihuaJulieZhu/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
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.
Getting started
Browse package contents
Package details |
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| Author | Lihua Julie Zhu, Jianhong Ou, Jun Yu, Hervé Pagès, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe and Michael Green |
| Bioconductor views | Annotation ChIPSeq ChIPchip |
| Maintainer | Lihua Julie Zhu <julie.zhu@umassmed.edu>, Jianhong Ou <ou.jianhong@gmail.com> |
| License | GPL (>= 2) |
| Version | 3.23.3 |
| Package repository | View on GitHub |
| Installation |
Install the latest version of this package by entering the following in R:
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