clusterProfiler

This is the development version of clusterProfiler; for the stable release version, see clusterProfiler.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8

A Universal Enrichment Tool for Interpreting Omics Data

Bioconductor version: Development (3.24)

A universal tool for interpreting functional characteristics of omics data. It supports Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA) for both coding and non-coding genomics data of thousands of species. It provides a unified and tidy interface to access, manipulate, and visualize enrichment results. A key capability is the simultaneous analysis and comparison of datasets from multiple treatments or time points. It also provides high-level access to topology-aware enrichment workflows powered by 'enrichit', including single-network and multi-layer network enrichment for Gene Ontology and KEGG analyses. Furthermore, it integrates Large Language Model (LLM) capabilities to provide automated and insightful interpretation of enrichment results.

Author: Guangchuang Yu [aut, cre, cph] ORCID: 0000-0002-6485-8781 , Li-Gen Wang [ctb], Xiao Luo [ctb], Meijun Chen [ctb], Giovanni Dall'Olio [ctb], Wanqian Wei [ctb], Chun-Hui Gao [ctb] ORCID: 0000-0002-1445-7939

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Guangchuang Yu. clusterProfiler: A Universal Enrichment Tool for Interpreting Omics Data. doi:10.18129/B9.bioc.clusterProfiler, R package version 4.21.3, https://bioconductor.org/packages/clusterProfiler.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

clusterProfiler.html	HTML
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Clustering, GO, GeneSetEnrichment, KEGG, MultipleComparison, Pathways, Reactome, Software, Visualization
Version	4.21.3
In Bioconductor since	BioC 2.8 (R-2.13) (15.5 years)
License	Artistic-2.0
Depends	R (>= 4.2.0)
Imports	aisdk, AnnotationDbi, dplyr, enrichit (>= 0.1.6), enrichplot (>= 1.9.3), ggplot2, GO.db, GOSemSim (>= 2.27.2), gson (>= 0.0.7), httr, igraph, jsonlite, magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.2.3)
System Requirements
URL	https://yulab-smu.top/contribution-knowledge-mining/
Bug Reports	https://github.com/YuLab-SMU/clusterProfiler/issues

Suggests	AnnotationHub, BiocManager, DOSE, ggtangle, readr, org.Hs.eg.db, quarto, testthat
Linking To
Enhances
Depends On Me	maEndToEnd
Imports Me	bioCancer, broadSeq, CaMutQC, CBNplot, CEMiTool, CeTF, damidBind, debrowser, DRviaSPCN, EasyCellType, epiregulon.extra, esATAC, ExpHunterSuite, exploreSE, famat, GDCRNATools, genekitr, GExPipe, gINTomics, GOaGO, goatea, goSorensen, GSEAlens, MetaPhOR, methylGSA, MicrobiomeProfiler, miRSM, miRspongeR, mitology, Moonlight2R, MoonlightR, mosdef, PanomiR, pathlinkR, PathwayVote, Pigengene, postNet, recountWorkflow, ReducedExperiment, RFLOMICS, TiDEomics, TraianProt, VISTA, vsclust, XYomics
Suggests Me	BenchHub, bregr, ChIPseeker, ClusterGVis, cola, DAPAR, DeeDeeExperiment, diffwrap, DOSE, easyEWAS, EMMA, enrichit, enrichplot, EpiCompare, EpiMix, epiSeeker, GeDi, GeneTonic, GenomicSuperSignature, GeoTcgaData, ggkegg, ggpicrust2, GOSemSim, grandR, GRaNIE, GSEAmining, IOBR, ivolcano, levi, mastR, MesKit, OlinkAnalyze, org.Mxanthus.db, pathdb, ReactomePA, ReporterScore, rrvgo, scFeatures, scGPS, scGraphVerse, SpliceImpactR, SRscore, SurprisalAnalysis, TCGAbiolinks, tidybulk, tinyarray, UKBAnalytica, venny, wikiprofiler
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	clusterProfiler_4.21.3.tar.gz
Windows Binary (x86_64)	clusterProfiler_4.21.3.zip
macOS Binary (big-sur-x86_64)	clusterProfiler_4.21.3.tgz
macOS Binary (sonoma-arm64)	clusterProfiler_4.21.3.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