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>

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

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

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