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Bioconductor - clusterProfiler

clusterProfiler

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

A universal enrichment tool for interpreting omics data

Bioconductor version: Release (3.21)

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] 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")): 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 Details biocViews Annotation, Clustering, GO, GeneSetEnrichment, KEGG, MultipleComparison, Pathways, Reactome, Software, Visualization Version 4.16.0 In Bioconductor since BioC 2.8 (R-2.13) (14 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 See More Suggests AnnotationHub, knitr, jsonlite, readr, rmarkdown, org.Hs.eg.db, prettydoc, BiocManager, testthat Linking To Enhances Depends On Me maEndToEnd Imports Me bioCancer, broadSeq, CaMutQC, CBNplot, CEMiTool, CeTF, debrowser, EasyCellType, EnrichDO, epiregulon.extra, esATAC, famat, GDCRNATools, gINTomics, goSorensen, MetaPhOR, methylGSA, MicrobiomeProfiler, miRSM, miRspongeR, Moonlight2R, MoonlightR, mosdef, PanomiR, pathlinkR, Pigengene, ReducedExperiment, RFLOMICS, seqArchRplus, signatureSearch, ExpHunterSuite, recountWorkflow, DRviaSPCN, genekitr, Grouphmap, immcp, pathwayTMB, PathwayVote, PMAPscore, RVA, ssdGSA, tinyarray Suggests Me ChIPseeker, cola, DAPAR, DOSE, enrichplot, EpiCompare, EpiMix, GeDi, GeneTonic, GenomicSuperSignature, GeoTcgaData, ggkegg, GOSemSim, GRaNIE, GSEAmining, mastR, MesKit, mitology, ReactomePA, rrvgo, scFeatures, scGPS, TCGAbiolinks, tidybulk, vsclust, org.Mxanthus.db, GeneSelectR, ggpicrust2, grandR, MARVEL, OlinkAnalyze, ReporterScore, SCpubr Links To Me Build Report Build Report Package Archives

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

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