ChIPpeakAnno

This is the development version of ChIPpeakAnno; for the stable release version, see 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: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Annotation, ChIPSeq, ChIPchip, Software
Version 3.39.0
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), 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
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, 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, 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_3.39.0.tar.gz
Windows Binary ChIPpeakAnno_3.39.0.zip (64-bit only)
macOS Binary (x86_64) ChIPpeakAnno_3.39.0.tgz
macOS Binary (arm64) ChIPpeakAnno_3.39.0.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