clusterProfiler
A universal enrichment tool for interpreting omics data
Bioconductor version: Release (3.17)
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("clusterProfiler")):
Installation
To install this package, start R (version "4.3") 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")| Statistical analysis and visualization of functional profiles for genes and gene clusters | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Clustering, GO, GeneSetEnrichment, KEGG, MultipleComparison, Pathways, Reactome, Software, Visualization |
| Version | 4.8.2 |
| In Bioconductor since | BioC 2.8 (R-2.13) (12.5 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(>= 2.26.1), gson (>= 0.0.7), magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils |
| Linking To | |
| Suggests | AnnotationHub, knitr, rmarkdown, org.Hs.eg.db, prettydoc, ReactomePA, testthat |
| System Requirements | |
| Enhances | |
| URL | https://yulab-smu.top/biomedical-knowledge-mining-book/(docs) https://doi.org/10.1016/j.xinn.2021.100141(paper) |
| Bug Reports | https://github.com/GuangchuangYu/clusterProfiler/issues |
See More
| Depends On Me | maEndToEnd |
| Imports Me | bioCancer, CBNplot, CEMiTool, CeTF, debrowser, EasyCellType, eegc, enrichTF, esATAC, ExpHunterSuite, famat, fcoex, GDCRNATools, goSorensen, IRISFGM, MAGeCKFlute, MetaPhOR, methylGSA, MicrobiomeProfiler, miRspongeR, MoonlightR, multiSight, netboxr, PanomiR, PFP, Pigengene, recountWorkflow, seqArchRplus, signatureSearch, TCGAWorkflow, TimiRGeN |
| Suggests Me | ChIPseeker, cola, DAPAR, DOSE, enrichplot, EpiCompare, epihet, EpiMix, GeneTonic, GenomicSuperSignature, GeoTcgaData, GOSemSim, GRaNIE, GSEAmining, mastR, MesKit, org.Mxanthus.db, paxtoolsr, ReactomePA, rrvgo, scFeatures, 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_4.8.2.tar.gz |
| Windows Binary | clusterProfiler_4.8.2.zip |
| macOS Binary (x86_64) | clusterProfiler_4.8.2.tgz |
| macOS Binary (arm64) | clusterProfiler_4.8.2.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 3.17 | Source Archive |