clusterProfiler

DOI: 10.18129/B9.bioc.clusterProfiler  

A universal enrichment tool for interpreting omics data

Bioconductor version: Release (3.16)

This package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios. It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation. Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions.

Author: Guangchuang Yu [aut, cre, cph] , Li-Gen Wang [ctb], Erqiang Hu [ctb], Xiao Luo [ctb], Meijun Chen [ctb], Giovanni Dall'Olio [ctb], Wanqian Wei [ctb], Chun-Hui Gao [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("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	4.6.2
In Bioconductor since	BioC 2.8 (R-2.13) (12 years)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	AnnotationDbi, downloader, DOSE(>= 3.23.2), dplyr, enrichplot(>= 1.9.3), GO.db, GOSemSim, gson (>= 0.0.7), magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils
LinkingTo
Suggests	AnnotationHub, knitr, rmarkdown, org.Hs.eg.db, prettydoc, ReactomePA, testthat
SystemRequirements
Enhances
URL	https://yulab-smu.top/biomedical-knowledge-mining-book/(docs) https://doi.org/10.1016/j.xinn.2021.100141(paper)
BugReports	https://github.com/GuangchuangYu/clusterProfiler/issues
Depends On Me	maEndToEnd
Imports Me	bioCancer, CEMiTool, CeTF, conclus, debrowser, EasyCellType, eegc, enrichTF, esATAC, ExpHunterSuite, famat, fcoex, GDCRNATools, goSorensen, IRISFGM, MAGeCKFlute, MetaPhOR, methylGSA, MicrobiomeProfiler, miRspongeR, MoonlightR, multiSight, netboxr, PanomiR, PFP, Pigengene, recountWorkflow, RNASeqR, signatureSearch, TCGAbiolinksGUI, TCGAWorkflow, TimiRGeN
Suggests Me	ChIPseeker, cola, DAPAR, DOSE, enrichplot, EpiCompare, epihet, EpiMix, GeneTonic, GenomicSuperSignature, GOSemSim, GRaNIE, GSEAmining, MesKit, org.Mxanthus.db, paxtoolsr, ReactomePA, rrvgo, scGPS, simplifyEnrichment, TCGAbiolinks, tidybulk, vsclust
Links To Me
Build Report

Package Archives

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

Source Package	clusterProfiler_4.6.2.tar.gz
Windows Binary	clusterProfiler_4.6.2.zip
macOS Binary (x86_64)	clusterProfiler_4.6.2.tgz
macOS Binary (arm64)	clusterProfiler_4.6.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/clusterProfiler
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/clusterProfiler
Bioc Package Browser	https://code.bioconductor.org/browse/clusterProfiler/
Package Short Url	https://bioconductor.org/packages/clusterProfiler/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive