DOI: 10.18129/B9.bioc.DOSE    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see DOSE.

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: 3.8

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>

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


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script 00 DOSE introduction
HTML R Script 01 DOSE semantic similarity analysis
HTML R Script 02 Disease enrichment analysis
HTML R Script 03 Disease GSEA
PDF   Reference Manual
Text   NEWS


biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization
Version 3.8.2
In Bioconductor since BioC 2.9 (R-2.14) (7.5 years)
License Artistic-2.0
Depends R (>= 3.4.0)
Imports AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim(>= 2.0.0), methods, qvalue, reshape2, S4Vectors, stats, utils
Suggests BiocStyle, clusterProfiler, knitr,, testthat
Depends On Me
Imports Me bioCancer, clusterProfiler, debrowser, eegc, enrichplot, facopy, GDCRNATools, LINC, MAGeCKFlute, meshes, miRsponge, MoonlightR, PathwaySplice, ReactomePA, RNASeqR
Suggests Me GOSemSim
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DOSE_3.8.2.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) DOSE_3.8.2.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: