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>

Citation (from within R, enter citation("clusterProfiler")):

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

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