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.

AuthorGuangchuang Yu <guangchuangyu@gmail.com> with contributions from Li-Gen Wang, Vladislav Petyuk and Giovanni Dall'Olio.
Date of publicationNone
MaintainerGuangchuang Yu <guangchuangyu@gmail.com>
LicenseArtistic-2.0
Version3.0.10
https://guangchuangyu.github.io/DOSE

View on Bioconductor

Functions

barplot.enrichResult Man page
clusterSim Man page
cnetplot Man page
cnetplot,enrichResult-method Man page
cnetplot,gseaResult-method Man page
cnetplot_internal Man page
computeIC Man page
DataSet Man page
DGN_EXTID2PATHID Man page
DGN_PATHID2EXTID Man page
DGN_PATHID2NAME Man page
DO2ALLEG Man page
DO2EG Man page
DOIC Man page
DOLite2EG Man page
DOLiteTerm Man page
DOSE Man page
DOSE-package Man page
doSim Man page
dotbl Man page
dotplot Man page
dotplot,enrichResult,ANY-method Man page
dotplot,enrichResult-method Man page
EG2ALLDO Man page
EG2DO Man page
EG2DOLite Man page
enrichDGN Man page
enrichDGNv Man page
enrichDO Man page
enricher_internal Man page
enrichMap Man page
enrichNCG Man page
enrichResult-class Man page
EXTID2NAME Man page
fortify.enrichResult Man page
fortify.gseaResult Man page
gene2DO Man page
geneID Man page
geneInCategory Man page
geneList Man page
geneSim Man page
gseahResult-class Man page
GSEA_internal Man page
gseaplot Man page
gseaResult-class Man page
gseDGN Man page
gseDO Man page
gseNCG Man page
gsfilter Man page
list2graph Man page
mclusterSim Man page
NCG_EXTID2PATHID Man page
NCG_PATHID2EXTID Man page
NCG_PATHID2NAME Man page
netplot Man page
plot Man page
plot,enrichResult,ANY-method Man page
plot,enrichResult-method Man page
plot,gseaResult,ANY-method Man page
plot,gseaResult-method Man page
rebuildAnnoData Man page
scaleNodeColor Man page
setReadable Man page
setting.graph.attributes Man page
show Man page
show,enrichResult-method Man page
show,gseaResult-method Man page
simplot Man page
summary Man page
summary,enrichResult-method Man page
summary,gseaResult-method Man page
theme_dose Man page
upsetplot Man page
upsetplot,enrichResult,ANY-method Man page
upsetplot,enrichResult-method Man page
VDGN_EXTID2PATHID Man page
VDGN_PATHID2EXTID Man page
VDGN_PATHID2NAME Man page

Files

DOSE/DESCRIPTION
DOSE/NAMESPACE
DOSE/NEWS
DOSE/R
DOSE/R/00-AllClasses.R DOSE/R/AllGenerics.R DOSE/R/DOSE-package.R DOSE/R/accessor.R DOSE/R/barplot.R DOSE/R/build_Anno.R DOSE/R/clusterSim.R DOSE/R/cnetplot.R DOSE/R/doSim.R DOSE/R/dotplot.R DOSE/R/enrichDGN.R DOSE/R/enrichDGNv.R DOSE/R/enrichDO.R DOSE/R/enrichDisease.R DOSE/R/enrichMap.R DOSE/R/enrichNCG.R DOSE/R/enrichResult.R DOSE/R/enricher_internal.R DOSE/R/geneSim.R DOSE/R/gseAnalyzer.R DOSE/R/gsea.R DOSE/R/gseaResult.R DOSE/R/gsfilter.R DOSE/R/mclusterSim.R DOSE/R/simplot.R DOSE/R/upsetplot.R DOSE/R/utilities.R DOSE/R/zzz.R
DOSE/README.md
DOSE/build
DOSE/build/vignette.rds
DOSE/data
DOSE/data/DGN_EXTID2PATHID.rda
DOSE/data/DGN_PATHID2EXTID.rda
DOSE/data/DGN_PATHID2NAME.rda
DOSE/data/DO2ALLEG.rda
DOSE/data/DO2EG.rda
DOSE/data/DOIC.rda
DOSE/data/DOLite2EG.rda
DOSE/data/DOLiteTerm.rda
DOSE/data/EG2ALLDO.rda
DOSE/data/EG2DO.rda
DOSE/data/EG2DOLite.rda
DOSE/data/NCG_EXTID2PATHID.rda
DOSE/data/NCG_PATHID2EXTID.rda
DOSE/data/NCG_PATHID2NAME.rda
DOSE/data/VDGN_EXTID2PATHID.rda
DOSE/data/VDGN_PATHID2EXTID.rda
DOSE/data/VDGN_PATHID2NAME.rda
DOSE/data/datalist
DOSE/data/dotbl.rda
DOSE/data/geneList.rda
DOSE/inst
DOSE/inst/CITATION
DOSE/inst/doc
DOSE/inst/doc/DOSE.R
DOSE/inst/doc/DOSE.Rmd
DOSE/inst/doc/DOSE.html
DOSE/inst/doc/GSEA.R
DOSE/inst/doc/GSEA.Rmd
DOSE/inst/doc/GSEA.html
DOSE/inst/doc/enrichmentAnalysis.R
DOSE/inst/doc/enrichmentAnalysis.Rmd
DOSE/inst/doc/enrichmentAnalysis.html
DOSE/inst/doc/semanticAnalysis.R
DOSE/inst/doc/semanticAnalysis.Rmd
DOSE/inst/doc/semanticAnalysis.html
DOSE/inst/extdata
DOSE/inst/extdata/build_DGN_Anno.R
DOSE/inst/extdata/build_NCG_Anno.R
DOSE/man
DOSE/man/DOSE-package.Rd DOSE/man/DataSet.Rd DOSE/man/EXTID2NAME.Rd DOSE/man/GSEA_internal.Rd DOSE/man/barplot.enrichResult.Rd DOSE/man/clusterSim.Rd DOSE/man/cnetplot-methods.Rd DOSE/man/cnetplot_internal.Rd DOSE/man/computeIC.Rd DOSE/man/doSim.Rd DOSE/man/dotplot-methods.Rd DOSE/man/enrichDGN.Rd DOSE/man/enrichDGNv.Rd DOSE/man/enrichDO.Rd DOSE/man/enrichMap.Rd DOSE/man/enrichNCG.Rd DOSE/man/enrichResult-class.Rd DOSE/man/enricher_internal.Rd DOSE/man/fortify.enrichResult.Rd DOSE/man/fortify.gseaResult.Rd DOSE/man/gene2DO.Rd DOSE/man/geneID.Rd DOSE/man/geneInCategory.Rd DOSE/man/geneSim.Rd DOSE/man/gseDGN.Rd DOSE/man/gseDO.Rd DOSE/man/gseNCG.Rd DOSE/man/gseaResult-class.Rd DOSE/man/gseaplot.Rd DOSE/man/gsfilter.Rd DOSE/man/list2graph.Rd DOSE/man/mclusterSim.Rd DOSE/man/netplot.Rd DOSE/man/plot-methods.Rd DOSE/man/rebuildAnnoData.Rd DOSE/man/scaleNodeColor.Rd DOSE/man/setReadable.Rd DOSE/man/setting.graph.attributes.Rd DOSE/man/show-methods.Rd DOSE/man/simplot.Rd DOSE/man/summary-methods.Rd DOSE/man/theme_dose.Rd DOSE/man/upsetplot-methods.Rd
DOSE/tests
DOSE/tests/testthat
DOSE/tests/testthat.R
DOSE/tests/testthat/test-doSim.R
DOSE/tests/testthat/test-gene2DO.R
DOSE/tests/testthat/test-geneSim.R
DOSE/vignettes
DOSE/vignettes/DOSE.Rmd
DOSE/vignettes/DOSE.bib
DOSE/vignettes/GSEA.Rmd
DOSE/vignettes/enrichmentAnalysis.Rmd
DOSE/vignettes/figures
DOSE/vignettes/figures/cnet_enrichDO.png
DOSE/vignettes/figures/cnet_gseNCG.png
DOSE/vignettes/figures/enrichMap_enrichDO.png
DOSE/vignettes/figures/enrichMap_gseNCG.png
DOSE/vignettes/figures/upsetplot_enrichDO.png
DOSE/vignettes/nature.csl
DOSE/vignettes/semanticAnalysis.Rmd

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