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)
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], 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
| Reference Manual |
Details
| biocViews | Annotation, Clustering, GO, GeneSetEnrichment, KEGG, MultipleComparison, Pathways, Reactome, Software, Visualization |
| Version | 4.17.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) (14.5 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 | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/clusterProfiler |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/clusterProfiler |
| Package Short Url | https://bioconductor.org/packages/clusterProfiler/ |
| Package Downloads Report | Download Stats |