DOSE: Disease Ontology Semantic and Enrichment analysis

Share:

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.

Author
Guangchuang Yu <guangchuangyu@gmail.com> with contributions from Li-Gen Wang, Vladislav Petyuk and Giovanni Dall'Olio.
Date of publication
None
Maintainer
Guangchuang Yu <guangchuangyu@gmail.com>
License
Artistic-2.0
Version
3.0.9
URLs

View on Bioconductor

Man pages

barplot.enrichResult
barplot
clusterSim
clusterSim
cnetplot_internal
cnetplot_internal
cnetplot-methods
cnetplot method
computeIC
compute information content
DataSet
Datasets
DOSE-package
Disease Ontology Semantic and Enrichment analysis Implemented...
doSim
doSim
dotplot-methods
dotplot method
enrichDGN
Enrichment analysis based on the DisGeNET (<URL:...
enrichDGNv
enrichDGN
enrichDO
DO Enrichment Analysis
enricher_internal
enrich.internal
enrichMap
enrichMap
enrichNCG
enrichNCG
enrichResult-class
Class "enrichResult" This class represents the result of...
EXTID2NAME
EXTID2NAME
fortify.enrichResult
fortify
fortify.gseaResult
fortify.gseaResult
gene2DO
convert Gene ID to DO Terms
geneID
geneID generic
geneInCategory
geneInCategory generic
geneSim
geneSim
GSEA_internal
GSEA_internal
gseaplot
visualize analyzing result of GSEA
gseaResult-class
Class "gseaResult" This class represents the result of GSEA...
gseDGN
DisGeNET Gene Set Enrichment Analysis
gseDO
DO Gene Set Enrichment Analysis
gseNCG
NCG Gene Set Enrichment Analysis
gsfilter
gsfilter
list2graph
convert gene IDs to igraph object
mclusterSim
mclusterSim
netplot
netplot
plot-methods
plot method
rebuildAnnoData
rebuiding annotation data
scaleNodeColor
scaleNodeColor
setReadable
setReadable
setting.graph.attributes
setting.graph.attributes
show-methods
show method
simplot
simplot
summary-methods
summary method
theme_dose
theme_dose
upsetplot-methods
upsetplot method

Files in this package

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