clusterProfiler

DOI: 10.18129/B9.bioc.clusterProfiler    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see clusterProfiler.

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

Bioconductor version: 3.12

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

Author: Guangchuang Yu [aut, cre, cph] , 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 (version "4.0") and enter:

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

BiocManager::install("clusterProfiler")

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("clusterProfiler")

 

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	3.18.1
In Bioconductor since	BioC 2.8 (R-2.13) (10 years)
License	Artistic-2.0
Depends	R (>= 3.4.0)
Imports	AnnotationDbi, downloader, DOSE(>= 3.13.1), dplyr, enrichplot(>= 1.9.3), GO.db, GOSemSim, magrittr, methods, plyr, qvalue, rlang, rvcheck, stats, tidyr, utils
LinkingTo
Suggests	AnnotationHub, knitr, org.Hs.eg.db, prettydoc, ReactomePA, testthat
SystemRequirements
Enhances
URL	https://yulab-smu.top/biomedical-knowledge-mining-book/
BugReports	https://github.com/GuangchuangYu/clusterProfiler/issues
Depends On Me	maEndToEnd
Imports Me	bioCancer, CEMiTool, CeTF, DAPAR, debrowser, eegc, enrichTF, esATAC, famat, fcoex, GDCRNATools, LINC, MAGeCKFlute, methylGSA, miRspongeR, MoonlightR, netboxr, recountWorkflow, RNASeqR, signatureSearch, TCGAbiolinksGUI, TCGAWorkflow, TimiRGeN
Suggests Me	ChIPseeker, cola, DOSE, enrichplot, epihet, GeneTonic, GOSemSim, GSEAmining, MesKit, org.Mxanthus.db, paxtoolsr, ReactomePA, rrvgo, scGPS, simplifyEnrichment, TCGAbiolinks, tidybulk
Links To Me
Build Report

Package Archives

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

Source Package	clusterProfiler_3.18.1.tar.gz
Windows Binary	clusterProfiler_3.18.1.zip
macOS 10.13 (High Sierra)	clusterProfiler_3.18.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/clusterProfiler
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/clusterProfiler
Package Short Url	https://bioconductor.org/packages/clusterProfiler/
Package Downloads Report	Download Stats