ChIPseeker

DOI: 10.18129/B9.bioc.ChIPseeker    

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

Bioconductor version: Release (3.15)

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], 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 "4.2") 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")

 

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

Details

biocViews Annotation, ChIPSeq, MultipleComparison, Software, Visualization
Version 1.32.1
In Bioconductor since BioC 2.14 (R-3.1) (8.5 years)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports AnnotationDbi, BiocGenerics, boot, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, ggVennDiagram, gplots, graphics, grDevices, gtools, methods, plotrix, dplyr, parallel, magrittr, RColorBrewer, rtracklayer, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils
LinkingTo
Suggests clusterProfiler, ggimage, ggplotify, ggupset, ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, tibble
SystemRequirements
Enhances
URL https://guangchuangyu.github.io/software/ChIPseeker
BugReports https://github.com/YuLab-SMU/ChIPseeker/issues
Depends On Me
Imports Me EpiCompare, esATAC, profileplyr, segmenter, 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_1.32.1.tar.gz
Windows Binary ChIPseeker_1.32.1.zip
macOS Binary (x86_64) ChIPseeker_1.32.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/ChIPseeker
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ChIPseeker
Package Short Url https://bioconductor.org/packages/ChIPseeker/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.15 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: