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This is the development version of DOSE; for the stable release version, see DOSE.

Disease Ontology Semantic and Enrichment analysis

Bioconductor version: Development (3.19)

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], Erqiang Hu [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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


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

# The following initializes usage of Bioc devel


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Reference Manual PDF


biocViews Annotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization
Version 3.29.2
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports AnnotationDbi, HDO.db, BiocParallel, fgsea, ggplot2, GOSemSim(>= 2.27.1), methods, qvalue, reshape2, stats, utils, yulab.utils
System Requirements
URL https://yulab-smu.top/biomedical-knowledge-mining-book/
Bug Reports https://github.com/GuangchuangYu/DOSE/issues
See More
Suggests prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, rmarkdown, org.Hs.eg.db, HPO.db, MPO.db, testthat
Linking To
Depends On Me
Imports Me bioCancer, clusterProfiler, debrowser, eegc, enrichplot, ExpHunterSuite, GDCRNATools, MAGeCKFlute, meshes, miRSM, miRspongeR, Moonlight2R, MoonlightR, pareg, Pigengene, ReactomePA, RegEnrich, scTensor, signatureSearch, SVMDO, TDbasedUFEadv
Suggests Me cola, GOSemSim, GRaNIE, rrvgo, scGPS, simplifyEnrichment
Links To Me
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Package Archives

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

Source Package DOSE_3.29.2.tar.gz
Windows Binary DOSE_3.29.2.zip
macOS Binary (x86_64) DOSE_3.29.2.tgz
macOS Binary (arm64) DOSE_3.29.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/DOSE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DOSE
Bioc Package Browser https://code.bioconductor.org/browse/DOSE/
Package Short Url https://bioconductor.org/packages/DOSE/
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