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DOSE

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DOSE")

Details

MaintainerGuangchuang Yu <guangchuangyu@gmail.com>
AuthorGuangchuang Yu [aut, cre], Li-Gen Wang [ctb], Vladislav Petyuk [ctb], Giovanni Dall'Olio [ctb]
LicenseArtistic-2.0
URLhttps://yulab-smu.top/contribution-knowledge-mining/
Bug Reportshttps://github.com/GuangchuangYu/DOSE/issues
Downloads rank26693
Source branchRELEASE_3_23
biocViewsAnnotation, GeneSetEnrichment, MultipleComparison, Pathways, Software, Visualization

Documentation

Download

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 (12): clusterProfiler, cola, enrichit, ggpicrust2, GOSemSim, GRaNIE, IOBR, rrvgo, scFeatures, scGPS, scGraphVerse, TDbasedUFEadv