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 (3.23)
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. Furthermore, it integrates Large Language Model (LLM) capabilities to provide automated and insightful interpretation of enrichment results.
Author: Guangchuang Yu [aut, cre, cph]
, Li-Gen Wang [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 "4.6") 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")| clusterProfiler.html | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | Annotation, Clustering, GO, GeneSetEnrichment, KEGG, MultipleComparison, Pathways, Reactome, Software, Visualization |
| Version | 4.19.6 |
| In Bioconductor since | BioC 2.8 (R-2.13) (15 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2.0) |
| Imports | AnnotationDbi, dplyr, enrichit (>= 0.1.1), 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 |
See More
| Suggests | AnnotationHub, BiocManager, DOSE, fanyi (>= 0.1.0), ggtangle, readr, org.Hs.eg.db, quarto, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | bioCancer, CaMutQC, CBNplot, CEMiTool, CeTF, damidBind, debrowser, EasyCellType, epiregulon.extra, GDCRNATools, goSorensen, MetaPhOR, methylGSA, miRSM, miRspongeR, mitology, Moonlight2R, MoonlightR, mosdef, PanomiR, pathlinkR, Pigengene, ReducedExperiment, RFLOMICS, vsclust, recountWorkflow, DRviaSPCN, genekitr, PathwayVote, SurprisalAnalysis, tinyarray, XYomics |
| Suggests Me | ChIPseeker, ClusterGVis, cola, DAPAR, DeeDeeExperiment, DOSE, enrichplot, EpiCompare, EpiMix, epiSeeker, GeDi, GeneTonic, GenomicSuperSignature, GeoTcgaData, ggkegg, GOSemSim, GRaNIE, GSEAmining, mastR, MesKit, MicrobiomeProfiler, ReactomePA, rrvgo, scFeatures, scGPS, scGraphVerse, TCGAbiolinks, tidybulk, org.Mxanthus.db, enrichit, ggpicrust2, grandR, ivolcano, OlinkAnalyze, ReporterScore, SRscore |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | clusterProfiler_4.19.6.tar.gz |
| Windows Binary (x86_64) | clusterProfiler_4.19.3.zip |
| macOS Binary (big-sur-x86_64) | clusterProfiler_4.19.2.tgz |
| macOS Binary (big-sur-arm64) | clusterProfiler_4.19.6.tgz |
| macOS Binary (sonoma-arm64) | |
| 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 |