Package: DOSE
Type: Package
Title: Disease Ontology Semantic and Enrichment analysis
Version: 4.7.2
Authors@R: c( person(given = "Guangchuang", family = "Yu",        email = "guangchuangyu@gmail.com",   role = c("aut", "cre")),
              person(given = "Li-Gen",      family = "Wang",      email = "reeganwang020@gmail.com",   role = "ctb"),
              person(given = "Vladislav",   family = "Petyuk",    email = "petyuk@gmail.com",          role = "ctb"),
              person(given = "Giovanni",    family = "Dall'Olio", email = "giovanni.dallolio@upf.edu", role = "ctb"))
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Description: 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.
Depends: R (>= 3.5.0)
Imports: AnnotationDbi, enrichit (>= 0.0.4), ggplot2, GOSemSim (>=
        2.39.2), gson (>= 0.0.5), memoise, methods, reshape2, utils,
        yulab.utils (> 0.2.2)
Suggests: clusterProfiler, knitr, org.Hs.eg.db, org.Mm.eg.db, quarto,
        testthat
VignetteBuilder: quarto
ByteCompile: true
License: Artistic-2.0
Encoding: UTF-8
URL: https://yulab-smu.top/contribution-knowledge-mining/
BugReports: https://github.com/GuangchuangYu/DOSE/issues
Packaged: 2026-07-15 20:48:46 UTC; root
biocViews: Annotation, Visualization, MultipleComparison,
        GeneSetEnrichment, Pathways, Software
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libuv1-dev
        libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-07-15 15:10:22 UTC
RemoteUrl: https://github.com/bioc/DOSE
RemoteRef: HEAD
RemoteSha: 43eb856d5f4d360c0141b54cf5fc5a13564628f2
NeedsCompilation: no
Author: Guangchuang Yu [aut, cre],
  Li-Gen Wang [ctb],
  Vladislav Petyuk [ctb],
  Giovanni Dall'Olio [ctb]