clusterProfiler
This is the development version of clusterProfiler; for the stable release version, see clusterProfiler.
A universal enrichment tool for interpreting omics data
Bioconductor version: Development (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:
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
citation("clusterProfiler")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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")| 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 | 4.15.1 |
| In Bioconductor since | BioC 2.8 (R-2.13) (13.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0) |
| 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, seqArchRplus, signatureSearch, ExpHunterSuite, recountWorkflow, TCGAWorkflow, DRviaSPCN, genekitr, Grouphmap, immcp, pathwayTMB, PMAPscore, RVA, ssdGSA, tinyarray |
| Suggests Me | ChIPseeker, cola, DAPAR, DOSE, enrichplot, EpiCompare, EpiMix, GeDi, GeneTonic, GenomicSuperSignature, GeoTcgaData, ggkegg, GOSemSim, GRaNIE, GSEAmining, mastR, MesKit, ReactomePA, rrvgo, scFeatures, scGPS, TCGAbiolinks, tidybulk, vsclust, org.Mxanthus.db, aPEAR, GeneSelectR, 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.
| Source Package | clusterProfiler_4.15.1.tar.gz |
| Windows Binary (x86_64) | clusterProfiler_4.15.1.zip (64-bit only) |
| macOS Binary (x86_64) | clusterProfiler_4.15.1.tgz |
| macOS Binary (arm64) | clusterProfiler_4.15.1.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 |