ChIPseeker

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

Bioconductor version: Release (3.17)

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

Author: Guangchuang Yu [aut, cre] , Ming Li [ctb], Qianwen Wang [ctb], Yun Yan [ctb], Hervé Pagès [ctb], Michael Kluge [ctb], Thomas Schwarzl [ctb], Zhougeng Xu [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Installation

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

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

BiocManager::install("ChIPseeker")

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("ChIPseeker")

ChIPseeker: an R package for ChIP peak Annotation, Comparison and Visualization	HTML	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	Annotation, ChIPSeq, MultipleComparison, Software, Visualization
Version	1.36.0
In Bioconductor since	BioC 2.14 (R-3.1) (9.5 years)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	AnnotationDbi, BiocGenerics, boot, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, methods, plotrix, dplyr, parallel, magrittr, rtracklayer, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, aplot, yulab.utils, tibble
Linking To
Suggests	clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, prettydoc
System Requirements
Enhances
URL	https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585
Bug Reports	https://github.com/YuLab-SMU/ChIPseeker/issues

Depends On Me
Imports Me	EpiCompare, esATAC, profileplyr, segmenter, seqArchRplus, TCGAWorkflow
Suggests Me	curatedAdipoChIP, GRaNIE
Links To Me
Build Report

Package Archives

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

Source Package	ChIPseeker_1.36.0.tar.gz
Windows Binary	ChIPseeker_1.36.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)	ChIPseeker_1.36.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ChIPseeker
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ChIPseeker
Bioc Package Browser	https://code.bioconductor.org/browse/ChIPseeker/
Package Short Url	https://bioconductor.org/packages/ChIPseeker/
Package Downloads Report	Download Stats