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 (3.24)
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. It also provides high-level access to topology-aware enrichment workflows powered by 'enrichit', including single-network and multi-layer network enrichment for Gene Ontology and KEGG analyses. 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 | 4.21.1 |
| In Bioconductor since | BioC 2.8 (R-2.13) (15.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2.0) |
| Imports | aisdk, AnnotationDbi, dplyr, enrichit (>= 0.1.6), 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
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | clusterProfiler_4.21.1.tar.gz |
| Windows Binary (x86_64) | clusterProfiler_4.21.1.zip |
| macOS Binary (big-sur-x86_64) | clusterProfiler_4.21.1.tgz |
| macOS Binary (sonoma-arm64) | clusterProfiler_4.21.1.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 |