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ChIPseeker

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization


Bioconductor version: Release (3.19)

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 "4.4") 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 1.40.0
In Bioconductor since BioC 2.14 (R-3.1) (10 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
System Requirements
URL https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585
Bug Reports https://github.com/YuLab-SMU/ChIPseeker/issues
See More
Suggests clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, prettydoc
Linking To
Enhances
Depends On Me
Imports Me esATAC, segmenter, seqArchRplus, TCGAWorkflow, cinaR
Suggests Me GRaNIE, curatedAdipoChIP
Links To Me
Build Report Build Report

Package Archives

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

Source Package ChIPseeker_1.40.0.tar.gz
Windows Binary ChIPseeker_1.40.0.zip
macOS Binary (x86_64) ChIPseeker_1.40.0.tgz
macOS Binary (arm64) ChIPseeker_1.40.0.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