Package: DOSE 4.7.3

Guangchuang Yu

DOSE: Disease Ontology Semantic and Enrichment analysis

Provides ontology-aware methods for disease and phenotype knowledge mining. DOSE supports semantic similarity analysis of disease and phenotype ontology terms, genes, and gene clusters using methods including Resnik, Schlicker, Jiang, Lin, and Wang. It also provides over-representation analysis and gene set enrichment analysis for interpreting gene vectors and ranked gene lists in disease, phenotype, and cancer contexts.

Authors:Guangchuang Yu [aut, cre], Li-Gen Wang [ctb], Vladislav Petyuk [ctb], Giovanni Dall'Olio [ctb]

DOSE_4.7.3.tar.gz
DOSE_4.7.3.zip(r-4.7-any)DOSE_4.7.3.zip(r-4.6-any)DOSE_4.7.3.zip(r-4.5-any)
DOSE_4.7.3.tgz(r-4.6-any)DOSE_4.7.3.tgz(r-4.5-any)
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DOSE_4.7.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DOSE/json (API)

# Install 'DOSE' in R:

install.packages('DOSE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/guangchuangyu/dose/issues

Datasets:

geneList - Datasets

On BioConductor:DOSE-4.7.3(bioc 3.24)DOSE-4.6.0(bioc 3.23)

annotation visualization multiplecomparison genesetenrichment pathways software disease-ontology enrichment-analysis semantic-similarity quarto

15.66 score 125 stars 75 packages 3.1k scripts 53k downloads 138 mentions 23 exports 63 dependencies

Last updated from:5846d72fe0. Checks:8 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	221
linux-devel	ERROR	411
source / vignettes	OK	358
linux-release	ERROR	343
macos-release	ERROR	257
macos-oldrel	ERROR	236
windows-devel	ERROR	261
windows-release	ERROR	301
windows-oldrel	ERROR	304
wasm-release	OK	190

Exports:as.data.frame clusterSim doseInterpretResult doseSim doSim enrichDO enrichNCG evidence explainDisease facet_grid gene2DO geneSim get_organism gseDO gseNCG interpretDisease mclusterSim rankMouseModels set_auto_update show simplot summary theme_dose

Dependencies:AnnotationDbi askpass Biobase BiocBaseUtils BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI digest enrichit farver fastmap fs generics ggplot2 glue GO.db GOSemSim gson gtable httr IRanges isoband jsonlite KEGGREST labeling lattice lifecycle magrittr Matrix memoise mime openssl pkgconfig plyr png R6 rappdirs RColorBrewer Rcpp RcppEigen reshape2 rlang RSQLite S4Vectors S7 scales Seqinfo stringi stringr sys vctrs viridisLite withr XVector yulab.utils

DOSE

Rendered fromDOSE.qmdusingquarto::html

Last update: 2026-06-30
Started: 2026-06-30

Help page	Topics
Coerce a canonical interpretation result to a data.frame	as.data.frame,doseInterpretResult-method
clusterSim	clusterSim
compute information content	computeIC
Datasets	DataSet geneList
Shared parameters for DOSE functions	dose_params
Construct a canonical interpretation result	doseInterpretResult
Canonical interpretation result class	doseInterpretResult-class
doseSim	doseSim doSim
DO Enrichment Analysis	enrichDO
enrichNCG	enrichNCG
Filter evidence rows from a canonical interpretation result	evidence evidence,doseInterpretResult-method
Add evidence-grounded explanation text to a canonical interpretation result	explainDisease
convert Gene ID to DO Terms	gene2DO
geneSim	geneSim
DO Gene Set Enrichment Analysis	gseDO
NCG Gene Set Enrichment Analysis	gseNCG
High-level disease interpretation entry point	interpretDisease
mclusterSim	mclusterSim
Rank mouse disease models from human query genes	rankMouseModels
Show a canonical interpretation result	show,doseInterpretResult-method
simplot	simplot
Summarize a canonical interpretation result	summary,doseInterpretResult-method
theme_dose	theme_dose

Package: DOSE 4.7.3

DOSE: Disease Ontology Semantic and Enrichment analysis

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