Package: DOSE 4.1.0

Guangchuang Yu

DOSE: Disease Ontology Semantic and Enrichment analysis

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.

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

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DOSE.pdf |DOSE.html✨
DOSE/json (API)
NEWS

# 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:

On BioConductor:DOSE-4.1.0(bioc 3.21)DOSE-4.0.0(bioc 3.20)

annotationvisualizationmultiplecomparisongenesetenrichmentpathwayssoftwaredisease-ontologyenrichment-analysissemantic-similarity

15.01 score 118 stars 61 packages 2.0k scripts 29k downloads 138 mentions 24 exports 85 dependencies

Last updated 4 months agofrom:898262a312. Checks:6 OK, 1 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
R-4.5-winOKJan 28 2025
R-4.5-linuxERRORJan 28 2025
R-4.4-winOKJan 28 2025
R-4.4-macOKJan 28 2025
R-4.3-winOKJan 28 2025
R-4.3-macOKJan 28 2025

Exports:clusterSimdoseSimdoSimenrichDGNenrichDGNvenrichDOenrichNCGEXTID2NAMEfacet_gridgene2DOgeneIDgeneInCategorygeneSimgseDGNgseDOgseNCGgsfiltermclusterSimparse_ratiosetReadableshowsimplotsummarytheme_dose

Dependencies:AnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcachemclicodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdigestfansifarverfastmapfastmatchfgseaformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggplot2glueGO.dbGOSemSimgtablehttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppreshape2rlangRSQLiteS4VectorsscalessnowstringistringrsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectoryulab.utils

DOSE: Disease Ontology Semantic and Enrichment analysis

Guangchuang Yu

Rendered fromDOSE.Rmdusingknitr::rmarkdownon Jan 28 2025.

Last update: 2020-09-09
Started: 2015-06-24

Readme and manuals

Help Manual

Help pageTopics
clusterSimclusterSim
Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.compareClusterResult-class plot,compareClusterResult-method show,compareClusterResult-method summary,compareClusterResult-method
compute information contentcomputeIC
DatasetsDataSet DGN_EXTID2PATHID DGN_PATHID2EXTID DGN_PATHID2NAME geneList NCG_EXTID2PATHID NCG_PATHID2EXTID NCG_PATHID2NAME VDGN_EXTID2PATHID VDGN_PATHID2EXTID VDGN_PATHID2NAME
doseSimdoseSim doSim
Enrichment analysis based on the DisGeNET (<http://www.disgenet.org/>)enrichDGN
enrichDGNenrichDGNv
DO Enrichment AnalysisenrichDO
enrich.internalenricher_internal
enrichNCGenrichNCG
Class "enrichResult" This class represents the result of enrichment analysis.enrichResult-class show,enrichResult-method summary,enrichResult-method
EXTID2NAMEEXTID2NAME
convert Gene ID to DO Termsgene2DO
geneID genericgeneID
geneInCategory genericgeneInCategory
geneSimgeneSim
GSEA_internalGSEA_internal
Class "gseaResult" This class represents the result of GSEA analysisgseahResult-class gseaResult-class show,gseaResult-method summary,gseaResult-method
DisGeNET Gene Set Enrichment AnalysisgseDGN
DO Gene Set Enrichment AnalysisgseDO
NCG Gene Set Enrichment AnalysisgseNCG
gsfiltergsfilter
mclusterSimmclusterSim
parse_ratioparse_ratio
setReadablesetReadable
show methodshow
simplotsimplot
summary methodsummary
theme_dosetheme_dose