Welcome to the new bioconductor.org!

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 (3.18)

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 <jianhong.ou at duke.edu>, Lihua Julie Zhu <julie.zhu at umassmed.edu>

Citation (from within R, enter citation("ChIPpeakAnno")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
ChIPpeakAnno Annotation Pipeline HTML R Script
ChIPpeakAnno FAQs HTML R Script
ChIPpeakAnno Quick Start HTML R Script
ChIPpeakAnno Vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, ChIPSeq, ChIPchip, Software
Version 3.36.1
In Bioconductor since BioC 2.5 (R-2.10) (14.5 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, InteractionSet, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils
System Requirements
URL
See More
Suggests AnnotationHub, 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
Linking To
Enhances
Depends On Me REDseq, vulcan
Imports Me ATACseqQC, DEScan2, GUIDEseq
Suggests Me chipseqDB, hicVennDiagram, R3CPET, seqsetvis
Links To Me
Build Report Build Report

Package Archives

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

Source Package ChIPpeakAnno_3.36.1.tar.gz
Windows Binary ChIPpeakAnno_3.36.1.zip
macOS Binary (x86_64) ChIPpeakAnno_3.36.1.tgz
macOS Binary (arm64) ChIPpeakAnno_3.36.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/ChIPpeakAnno
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ChIPpeakAnno
Bioc Package Browser https://code.bioconductor.org/browse/ChIPpeakAnno/
Package Short Url https://bioconductor.org/packages/ChIPpeakAnno/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive