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DOI: 10.18129/B9.bioc.ChIPpeakAnno    

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 (3.5)

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.

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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HTML R Script ChIPpeakAnno Annotation Pipeline
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biocViews Annotation, ChIPSeq, ChIPchip, Software
Version 3.10.2
In Bioconductor since BioC 2.5 (R-2.10) (8 years)
License GPL (>= 2)
Depends R (>= 3.2), methods, grid, IRanges(>= 2.5.27), Biostrings, GenomicRanges(>= 1.23.16), S4Vectors(>= 0.9.25), VennDiagram
Imports BiocGenerics(>= 0.1.0), GO.db, biomaRt, BSgenome, GenomicFeatures, GenomeInfoDb, matrixStats, AnnotationDbi, limma, multtest, RBGL, graph, BiocInstaller, stats, regioneR, DBI, ensembldb, Biobase, seqinr, idr, GenomicAlignments, DelayedArray, SummarizedExperiment, Rsamtools
Suggests reactome.db, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19,,, 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, BiocStyle, rtracklayer, knitr, rmarkdown, BiocStyle, testthat, trackViewer, motifStack, OrganismDbi
Depends On Me REDseq
Imports Me ATACseqQC, DChIPRep, FunciSNP, GUIDEseq, REDseq
Suggests Me oneChannelGUI, R3CPET, RIPSeeker
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