clusterProfiler

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see clusterProfiler.

A universal enrichment tool for interpreting omics data

Bioconductor version: 3.13

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] , Li-Gen Wang [ctb], Erqiang Hu [ctb], Meijun Chen [ctb], Giovanni Dall'Olio [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Installation

To install this package, start R (version "4.1") 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 4.0.5

In Bioconductor since BioC 2.8 (R-2.13) (13 years)

License Artistic-2.0

Depends R (>= 3.5.0)

Imports AnnotationDbi, downloader, DOSE(>= 3.13.1), dplyr, enrichplot(>= 1.9.3), GO.db, GOSemSim, magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils, yulab.utils

System Requirements

URL https://yulab-smu.top/biomedical-knowledge-mining-book/

Bug Reports https://github.com/GuangchuangYu/clusterProfiler/issues

Suggests AnnotationHub, knitr, rmarkdown, org.Hs.eg.db, prettydoc, ReactomePA, testthat

Linking To

Enhances

Depends On Me maEndToEnd