clusterProfiler

DOI: 10.18129/B9.bioc.clusterProfiler    

statistical analysis and visualization of functional profiles for genes and gene clusters

Bioconductor version: Release (3.6)

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

Author: Guangchuang Yu [aut, cre], Li-Gen Wang [ctb], Giovanni Dall'Olio [ctb] (formula interface of compareCluster)

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("clusterProfiler")

Documentation

HTML	R Script	Statistical analysis and visualization of functional profiles for genes and gene clusters
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Clustering, GO, GeneSetEnrichment, KEGG, MultipleComparison, Pathways, Reactome, Software, Visualization
Version	3.6.0
In Bioconductor since	BioC 2.8 (R-2.13) (7 years)
License	Artistic-2.0
Depends	R (>= 3.3.1), DOSE(>= 3.3.2)
Imports	AnnotationDbi, ggplot2, GO.db, GOSemSim(>= 2.0.0), magrittr, methods, plyr, qvalue, rvcheck, stats, stats4, tidyr, utils
LinkingTo
Suggests	AnnotationHub, GSEABase, KEGG.db, knitr, org.Hs.eg.db, prettydoc, pathview, ReactomePA, testthat, topGO
SystemRequirements
Enhances
URL	https://guangchuangyu.github.io/clusterProfiler
BugReports	https://github.com/GuangchuangYu/clusterProfiler/issues
Depends On Me
Imports Me	bioCancer, CEMiTool, DAPAR, debrowser, eegc, esATAC, LINC, miRsponge, MoonlightR, TCGAbiolinksGUI
Suggests Me	ChIPseeker, DOSE, GOSemSim, isomiRs, ReactomePA, TCGAbiolinks
Build Report

Package Archives

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

Source Package	clusterProfiler_3.6.0.tar.gz
Windows Binary	clusterProfiler_3.6.0.zip
Mac OS X 10.11 (El Capitan)	clusterProfiler_3.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/clusterProfiler
Package Short Url	http://bioconductor.org/packages/clusterProfiler/
Package Downloads Report	Download Stats