ChIPpeakAnno

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

Bioconductor version: Release (3.20)

The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities.

Author: Lihua Julie Zhu, Jianhong Ou, Jun Yu, Kai Hu, Haibo Liu, Junhui Li, Hervé Pagès, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe, Michael Green

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>, Lihua Julie Zhu <julie.zhu at umassmed.edu>, Kai Hu <kai.hu at umassmed.edu>, Junhui Li <junhui.li at umassmed.edu>

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

Installation

To install this package, start R (version "4.4") 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: annotate, visualize, and compare peak data	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, ChIPSeq, ChIPchip, Software
Version	3.40.0
In Bioconductor since	BioC 2.5 (R-2.10) (15 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), pwalign, DBI, dplyr, GenomeInfoDb, GenomicAlignments, GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics, grid, InteractionSet, KEGGREST, matrixStats, multtest, regioneR, rtracklayer, stats, utils, universalmotif, stringr, tibble, tidyr, data.table, scales, ensembldb
System Requirements
URL

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, EnsDb.Hsapiens.v86, TxDb.Hsapiens.UCSC.hg18.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR, knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack, OrganismDbi, BiocFileCache
Linking To
Enhances
Depends On Me	REDseq, csawBook
Imports Me	ATACseqQC, DEScan2, GUIDEseq
Suggests Me	hicVennDiagram, R3CPET, seqsetvis, chipseqDB
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	ChIPpeakAnno_3.40.0.tar.gz
Windows Binary (x86_64)	ChIPpeakAnno_3.40.0.zip (64-bit only)
macOS Binary (x86_64)	ChIPpeakAnno_3.40.0.tgz
macOS Binary (arm64)	ChIPpeakAnno_3.39.3.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