clusterProfiler

This is the released version of clusterProfiler; for the devel version, see clusterProfiler.

A universal enrichment tool for interpreting omics data

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DOI: 10.18129/B9.bioc.clusterProfiler

Bioconductor version: Release (3.22)

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 universal 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] ORCID iD 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 iD ORCID: 0000-0002-1445-7939

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Installation

To install this package, start R (version "4.5") 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 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 4.18.1

In Bioconductor since BioC 2.8 (R-2.13) (14.5 years)

License Artistic-2.0

Depends R (>= 4.2.0)

Imports AnnotationDbi, DOSE(>= 3.23.2), dplyr, enrichplot(>= 1.9.3), GO.db, GOSemSim(>= 2.27.2), gson (>= 0.0.7), httr, igraph, magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.1.6)

System Requirements

URL https://yulab-smu.top/contribution-knowledge-mining/

Bug Reports https://github.com/YuLab-SMU/clusterProfiler/issues

Suggests AnnotationHub, knitr, jsonlite, readr, rmarkdown, org.Hs.eg.db, prettydoc, BiocManager, testthat

Linking To

Enhances

Depends On Me maEndToEnd

Suggests Me ChIPseeker, cola, DAPAR, DeeDeeExperiment, DOSE, enrichplot, EpiCompare, EpiMix, GenomicSuperSignature, GeoTcgaData, ggkegg, GOSemSim, GRaNIE, GSEAmining, mastR, MesKit, ReactomePA, rrvgo, scGPS, scGraphVerse, TCGAbiolinks, tidybulk, org.Mxanthus.db, ClusterGVis, ggpicrust2, grandR, OlinkAnalyze, ReporterScore

Links To Me

Build Report Build Report

Package Archives

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

Source Package clusterProfiler_4.18.1.tar.gz

Windows Binary (x86_64) clusterProfiler_4.17.0.zip (64-bit only)

macOS Binary (x86_64) clusterProfiler_4.18.1.tgz

macOS Binary (arm64) clusterProfiler_4.18.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/clusterProfiler

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/clusterProfiler

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 3.22 Source Archive