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

Bioconductor version: Release (3.2)

The package is to facilitate the downstream analysis for ChIP-seq experiments. It includes functions to find the nearest gene, exon, miRNA or custom features such as the most conserved elements and other transcription factor binding sites supplied by users, retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms or pathways. 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). Starting 3.4, we also implement functions for permutation test to determine the association between two sets of peaks, and to plot heatmaps for given feature/peak ranges. This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages.

Author: Lihua Julie Zhu, Jianhong Ou, Jun Yu, Herve Pages, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe and Michael Green

Maintainer: Lihua Julie Zhu <julie.zhu at>, Jianhong Ou <Jianhong.ou at>

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biocViews Annotation, ChIPSeq, ChIPchip, Software
Version 3.4.1
In Bioconductor since BioC 2.5 (R-2.10) (6 years)
License GPL (>= 2)
Depends R (>= 3.1), methods, grid, IRanges, Biostrings, GenomicRanges, S4Vectors, VennDiagram
Imports BiocGenerics(>= 0.1.0), GO.db, biomaRt, BSgenome, GenomicFeatures, GenomeInfoDb, matrixStats, AnnotationDbi, limma, multtest, RBGL, graph, BiocInstaller, stats, regioneR, DBI, ensembldb, Biobase
Suggests reactome.db, BSgenome.Ecoli.NCBI.20080805,,, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, RUnit, BiocStyle, rtracklayer, knitr
Depends On Me ggtut, REDseq
Imports Me FunciSNP, GUIDEseq, REDseq
Suggests Me ggtut, oneChannelGUI, R3CPET, RIPSeeker
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