DOSE
This is the released version of DOSE; for the devel version, see DOSE.
All Bioconductor versions of DOSE
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9
Disease Ontology Semantic and Enrichment analysis
Bioconductor version: 3.23 · Package version: 4.6.0
This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.
Author: Guangchuang Yu [aut, cre], Li-Gen Wang [ctb], Vladislav Petyuk [ctb], Giovanni Dall'Olio [ctb]
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
Citation
From within R, enter citation("DOSE"):
Guangchuang Yu. DOSE: Disease Ontology Semantic and Enrichment analysis. doi:10.18129/B9.bioc.DOSE, R package version 4.6.0, https://bioconductor.org/packages/DOSE.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DOSE")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 4.6.0 |
| License | Artistic-2.0 |
| URL | https://yulab-smu.top/contribution-knowledge-mining/ |
| Bug Reports | https://github.com/GuangchuangYu/DOSE/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 2.9 (R-2.14) (14 years) |
| Downloads rank | 30 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/DOSE/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DOSE")| DOSE: Disease Ontology Semantic and Enrichment analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | DOSE_4.6.0.tar.gz |
| Windows binary (x86_64) | DOSE_4.5.0.zip |
| macOS binary (arm64) | DOSE_4.6.0.tgz |
| macOS binary (x86_64) | DOSE_4.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DOSE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DOSE |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 3.5.0)
Imports: AnnotationDbi, enrichit (>= 0.0.4), ggplot2, GOSemSim (>= 2.37.1), methods, reshape2, utils, yulab.utils (> 0.2.2)
Suggests: prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise, org.Hs.eg.db, rmarkdown, testthat
Reverse dependencies
Imports Me (17): bioCancer, debrowser, enrichplot, ExpHunterSuite, GDCRNATools, GOaGO, goatea, miRSM, miRspongeR, Moonlight2R, MoonlightR, Pigengene, RegEnrich, scTensor, signatureSearch, SVMDO, vsclust
Suggests Me (13): clusterProfiler, cola, enrichit, ggpicrust2, GOSemSim, GRaNIE, IOBR, rrvgo, scFeatures, scGPS, scGraphVerse, TDbasedUFEadv, wikiprofiler