ChIPpeakAnno

DOI: 10.18129/B9.bioc.ChIPpeakAnno    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see 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: 3.12

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, Kai Hu, Haibo Liu, Hervé Pagès, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe and Michael Green

Maintainer: Jianhong Ou <ou.jianhong at gmail.com>, Lihua Julie Zhu <julie.zhu at umassmed.edu>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ChIPpeakAnno")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ChIPpeakAnno")

 

HTML	R Script	ChIPpeakAnno Annotation Pipeline
HTML	R Script	ChIPpeakAnno FAQs
HTML	R Script	ChIPpeakAnno Quick Start
HTML	R Script	ChIPpeakAnno Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, ChIPSeq, ChIPchip, Software
Version	3.24.2
In Bioconductor since	BioC 2.5 (R-2.10) (11.5 years)
License	GPL (>= 2)
Depends	R (>= 3.5), methods, IRanges(>= 2.13.12), GenomicRanges(>= 1.31.8), S4Vectors(>= 0.17.25)
Imports	AnnotationDbi, BiocGenerics(>= 0.1.0), Biostrings(>= 2.47.6), DBI, dplyr, ensembldb, GenomeInfoDb, GenomicAlignments, GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics, grid, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils
LinkingTo
Suggests	BSgenome, limma, reactome.db, BiocManager, BiocStyle, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi
SystemRequirements
Enhances
URL
Depends On Me	REDseq, vulcan
Imports Me	ATACseqQC, DEScan2, FunciSNP, GUIDEseq
Suggests Me	chipseqDB, R3CPET, seqsetvis
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ChIPpeakAnno_3.24.2.tar.gz
Windows Binary	ChIPpeakAnno_3.24.2.zip
macOS 10.13 (High Sierra)	ChIPpeakAnno_3.24.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ChIPpeakAnno
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ChIPpeakAnno
Package Short Url	https://bioconductor.org/packages/ChIPpeakAnno/
Package Downloads Report	Download Stats