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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DOSE")
AuthorGuangchuang Yu [aut, cre], Li-Gen Wang [ctb], Vladislav Petyuk [ctb], Giovanni Dall'Olio [ctb]
Bioconductor views Annotation GeneSetEnrichment MultipleComparison Pathways Software Visualization
Date of publicationNone
MaintainerGuangchuang Yu <guangchuangyu@gmail.com>
LicenseArtistic-2.0
Version3.2.0
https://guangchuangyu.github.io/DOSE

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

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

gsInfo: gsInfo

list2graph: convert gene IDs to igraph object

mclusterSim: mclusterSim

netplot: netplot

plot-methods: plot method

rebuildAnnoData: rebuiding annotation data

reexports: Objects exported from other packages

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

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
dotplot,gseaResult,ANY-method Man page
dotplot,gseaResult-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
facet_grid Man page
fortify.enrichResult 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
gsInfo 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
reexports 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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.