Files in patzaw/BED
Biological Entity Dictionary (BED)
.Rbuildignore
.gitattributes
.gitignore
BED.Rproj
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/BED.R
R/BEIDList.R
R/beIDsToAllScopes.R
R/bedCall.R
R/bedImport.R
R/beidsModule.R
R/cacheBedCall.R
R/cacheBedResult.R
R/checkBeIds.R
R/checkBedCache.R
R/checkBedConn.R
R/cleanDubiousXRef.R
R/clearBedCache.R
R/compareBedInstances.R
R/convBeIdLists.R
R/convBeIds.R
R/convDfBeIds.R
R/dumpEnsCore.R
R/dumpNcbiDb.R
R/dumpNcbiTax.R
R/dumpUniprotDb.R
R/exploreBe.R
R/exploreConvPath.R
R/findBe.R
R/findBeids.R
R/firstCommonUpstreamBe.R
R/genBePath.R
R/genProbePath.R
R/geneIDsToAllScopes.R
R/generics.R
R/getAllBeIdSources.R
R/getBeIdConvTable.R
R/getBeIdDescription.R
R/getBeIdNameTable.R
R/getBeIdNames.R
R/getBeIdSymbolTable.R
R/getBeIdSymbols.R
R/getBeIdURL.R
R/getBeIds.R
R/getDirectOrigin.R
R/getDirectProduct.R
R/getEnsemblGeneIds.R
R/getEnsemblPeptideIds.R
R/getEnsemblTranscriptIds.R
R/getGeneDescription.R
R/getHomTable.R
R/getNcbiGeneTransPep.R
R/getOrgNames.R
R/getRelevantIds.R
R/getTargetedBe.R
R/getTaxId.R
R/getUniprot.R
R/guessIdScope.R
R/identicalScopes.R
R/largestBeSource.R
R/listBe.R
R/listBeIdSources.R
R/listDBAttributes.R
R/listOrganisms.R
R/listPlatforms.R
R/loadBE.R
R/loadBENames.R
R/loadBESymbols.R
R/loadBEVersion.R
R/loadBeAttribute.R
R/loadBedModel.R
R/loadCodesFor.R
R/loadCorrespondsTo.R
R/loadHistory.R
R/loadIsAssociatedTo.R
R/loadIsExpressedAs.R
R/loadIsHomologOf.R
R/loadIsTranslatedIn.R
R/loadLuceneIndexes.R
R/loadNCBIEntrezGOFunctions.R
R/loadNcbiTax.R
R/loadOrganisms.R
R/loadPlf.R
R/loadProbes.R
R/lsBedCache.R
R/registerBEDB.R
R/searchBeid.R
R/searchId.R
R/setBedVersion.R
R/showBedDataModel.R
R/zzz.R
README.Rmd
README.md
_pkgdown.yml
docs/404.html
docs/BED.html
docs/LICENSE-text.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/BED.html
docs/articles/BED_files/htmltools-fill-0.5.8.1/fill.css
docs/articles/BED_files/htmlwidgets-1.6.4/htmlwidgets.js
docs/articles/BED_files/vis-9.1.0/add_css.txt
docs/articles/BED_files/vis-9.1.0/img/network/acceptDeleteIcon.png
docs/articles/BED_files/vis-9.1.0/img/network/addNodeIcon.png
docs/articles/BED_files/vis-9.1.0/img/network/backIcon.png
docs/articles/BED_files/vis-9.1.0/img/network/connectIcon.png
docs/articles/BED_files/vis-9.1.0/img/network/cross.png
docs/articles/BED_files/vis-9.1.0/img/network/cross2.png
docs/articles/BED_files/vis-9.1.0/img/network/deleteIcon.png
docs/articles/BED_files/vis-9.1.0/img/network/downArrow.png
docs/articles/BED_files/vis-9.1.0/img/network/editIcon.png
docs/articles/BED_files/vis-9.1.0/img/network/leftArrow.png
docs/articles/BED_files/vis-9.1.0/img/network/minus.png
docs/articles/BED_files/vis-9.1.0/img/network/plus.png
docs/articles/BED_files/vis-9.1.0/img/network/rightArrow.png
docs/articles/BED_files/vis-9.1.0/img/network/upArrow.png
docs/articles/BED_files/vis-9.1.0/img/network/zoomExtends.png
docs/articles/BED_files/vis-9.1.0/vis-network.min.css
docs/articles/BED_files/vis-9.1.0/vis-network.min.js
docs/articles/BED_files/visNetwork-binding-2.1.2/visNetwork.js
docs/articles/img/BED-data-model.png
docs/articles/img/BED.png
docs/articles/index.html
docs/authors.html
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.3.1/bootstrap.min.css
docs/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js
docs/deps/clipboard.js-2.0.11/clipboard.min.js
docs/deps/data-deps.txt
docs/deps/font-awesome-6.4.2/css/all.css
docs/deps/font-awesome-6.4.2/css/all.min.css
docs/deps/font-awesome-6.4.2/css/v4-shims.css
docs/deps/font-awesome-6.4.2/css/v4-shims.min.css
docs/deps/font-awesome-6.4.2/webfonts/fa-brands-400.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-brands-400.woff2
docs/deps/font-awesome-6.4.2/webfonts/fa-regular-400.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-regular-400.woff2
docs/deps/font-awesome-6.4.2/webfonts/fa-solid-900.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-solid-900.woff2
docs/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2
docs/deps/headroom-0.11.0/headroom.min.js
docs/deps/headroom-0.11.0/jQuery.headroom.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/deps/search-1.0.0/autocomplete.jquery.min.js
docs/deps/search-1.0.0/fuse.min.js
docs/deps/search-1.0.0/mark.min.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/katex-auto.js
docs/lightswitch.js
docs/link.svg
docs/news/index.html
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/BED.html
docs/reference/BEIDList.html
docs/reference/BEIDs.html
docs/reference/beIDsToAllScopes.html
docs/reference/bedCall.html
docs/reference/bedImport.html
docs/reference/beidsServer.html
docs/reference/beidsUI.html
docs/reference/cacheBedCall.html
docs/reference/cacheBedResult.html
docs/reference/checkBeIds.html
docs/reference/checkBedCache.html
docs/reference/checkBedConn.html
docs/reference/cleanDubiousXRef.html
docs/reference/clearBedCache.html
docs/reference/compareBedInstances.html
docs/reference/connectToBed.html
docs/reference/convBeIdLists.html
docs/reference/convBeIds.html
docs/reference/convDfBeIds.html
docs/reference/dumpEnsCore.html
docs/reference/dumpNcbiDb.html
docs/reference/dumpNcbiTax.html
docs/reference/dumpUniprotDb.html
docs/reference/exploreBe.html
docs/reference/exploreConvPath.html
docs/reference/figures/BED.png
docs/reference/filterByBEID.html
docs/reference/findBe.html
docs/reference/findBeids.html
docs/reference/firstCommonUpstreamBe.html
docs/reference/focusOnScope.BEIDList.html
docs/reference/focusOnScope.html
docs/reference/forgetBedConnection.html
docs/reference/genBePath.html
docs/reference/genProbePath.html
docs/reference/geneIDsToAllScopes.html
docs/reference/getAllBeIdSources.html
docs/reference/getBeIdConvTable.html
docs/reference/getBeIdDescription.html
docs/reference/getBeIdNameTable.html
docs/reference/getBeIdNames.html
docs/reference/getBeIdSymbolTable.html
docs/reference/getBeIdSymbols.html
docs/reference/getBeIdURL.html
docs/reference/getBeIds.html
docs/reference/getDirectOrigin.html
docs/reference/getDirectProduct.html
docs/reference/getEnsemblGeneIds.html
docs/reference/getEnsemblPeptideIds.html
docs/reference/getEnsemblTranscriptIds.html
docs/reference/getGeneDescription.html
docs/reference/getHomTable.html
docs/reference/getNcbiGeneTransPep.html
docs/reference/getOrgNames.html
docs/reference/getRelevantIds.html
docs/reference/getTargetedBe.html
docs/reference/getTaxId.html
docs/reference/getUniprot.html
docs/reference/guessIdOrigin.html
docs/reference/guessIdScope.html
docs/reference/identicalScopes.html
docs/reference/index.html
docs/reference/is.BEIDList.html
docs/reference/largestBeSource.html
docs/reference/listBe.html
docs/reference/listBeIdSources.html
docs/reference/listDBAttributes.html
docs/reference/listOrganisms.html
docs/reference/listPlatforms.html
docs/reference/loadBE.html
docs/reference/loadBENames.html
docs/reference/loadBESymbols.html
docs/reference/loadBEVersion.html
docs/reference/loadBeAttribute.html
docs/reference/loadBedModel.html
docs/reference/loadBedOtherIndexes.html
docs/reference/loadBedResult.html
docs/reference/loadCodesFor.html
docs/reference/loadCorrespondsTo.html
docs/reference/loadHistory.html
docs/reference/loadIsAssociatedTo.html
docs/reference/loadIsExpressedAs.html
docs/reference/loadIsHomologOf.html
docs/reference/loadIsTranslatedIn.html
docs/reference/loadLuceneIndexes.html
docs/reference/loadNCBIEntrezGOFunctions.html
docs/reference/loadNcbiTax.html
docs/reference/loadOrganisms.html
docs/reference/loadPlf.html
docs/reference/loadProbes.html
docs/reference/lsBedCache.html
docs/reference/lsBedConnections.html
docs/reference/metadata-set.html
docs/reference/metadata.html
docs/reference/registerBEDB.html
docs/reference/scope.html
docs/reference/scopes.html
docs/reference/searchBeid.html
docs/reference/searchId.html
docs/reference/setBedVersion.html
docs/reference/showBedDataModel.html
docs/search.json
docs/sitemap.xml
inst/CITATION
inst/Documentation/BED-Model/BED-lucene-v3.cql
inst/Documentation/BED-Model/BED-lucene-v5.cql
inst/Documentation/BED-Model/BED-model-v3.cql
inst/Documentation/BED-Model/BED-model-v5.cql
inst/Documentation/BED-Model/BED.html
inst/Documentation/BED-Model/BED.png
inst/Documentation/BED-Model/BEType.cql
inst/doc/BED.R
inst/doc/BED.Rmd
inst/doc/BED.html
inst/pkgdown.yml
inst/rstudio/addins.dcf
man/BED.Rd
man/BEIDList.Rd
man/BEIDs.Rd
man/beIDsToAllScopes.Rd
man/bedCall.Rd
man/bedImport.Rd
man/beidsServer.Rd
man/cacheBedCall.Rd
man/cacheBedResult.Rd
man/checkBeIds.Rd
man/checkBedCache.Rd
man/checkBedConn.Rd
man/cleanDubiousXRef.Rd
man/clearBedCache.Rd
man/compareBedInstances.Rd
man/connectToBed.Rd
man/convBeIdLists.Rd
man/convBeIds.Rd
man/convDfBeIds.Rd
man/dumpEnsCore.Rd
man/dumpNcbiDb.Rd
man/dumpNcbiTax.Rd
man/dumpUniprotDb.Rd
man/exploreBe.Rd
man/exploreConvPath.Rd
man/figures/BED.png
man/filterByBEID.Rd
man/findBe.Rd
man/findBeids.Rd
man/firstCommonUpstreamBe.Rd
man/focusOnScope.BEIDList.Rd
man/focusOnScope.Rd
man/forgetBedConnection.Rd
man/genBePath.Rd
man/genProbePath.Rd
man/geneIDsToAllScopes.Rd
man/getAllBeIdSources.Rd
man/getBeIdConvTable.Rd
man/getBeIdDescription.Rd
man/getBeIdNameTable.Rd
man/getBeIdNames.Rd
man/getBeIdSymbolTable.Rd
man/getBeIdSymbols.Rd
man/getBeIdURL.Rd
man/getBeIds.Rd
man/getDirectOrigin.Rd
man/getDirectProduct.Rd
man/getEnsemblGeneIds.Rd
man/getEnsemblPeptideIds.Rd
man/getEnsemblTranscriptIds.Rd
man/getGeneDescription.Rd
man/getHomTable.Rd
man/getNcbiGeneTransPep.Rd
man/getOrgNames.Rd
man/getRelevantIds.Rd
man/getTargetedBe.Rd
man/getTaxId.Rd
man/getUniprot.Rd
man/guessIdScope.Rd
man/identicalScopes.Rd
man/is.BEIDList.Rd
man/largestBeSource.Rd
man/listBe.Rd
man/listBeIdSources.Rd
man/listDBAttributes.Rd
man/listOrganisms.Rd
man/listPlatforms.Rd
man/loadBE.Rd
man/loadBENames.Rd
man/loadBESymbols.Rd
man/loadBEVersion.Rd
man/loadBeAttribute.Rd
man/loadBedModel.Rd
man/loadBedOtherIndexes.Rd
man/loadBedResult.Rd
man/loadCodesFor.Rd
man/loadCorrespondsTo.Rd
man/loadHistory.Rd
man/loadIsAssociatedTo.Rd
man/loadIsExpressedAs.Rd
man/loadIsHomologOf.Rd
man/loadIsTranslatedIn.Rd
man/loadLuceneIndexes.Rd
man/loadNCBIEntrezGOFunctions.Rd
man/loadNcbiTax.Rd
man/loadOrganisms.Rd
man/loadPlf.Rd
man/loadProbes.Rd
man/lsBedCache.Rd
man/lsBedConnections.Rd
man/metadata-set.Rd
man/metadata.Rd
man/registerBEDB.Rd
man/scope.Rd
man/scopes.Rd
man/searchBeid.Rd
man/searchId.Rd
man/setBedVersion.Rd
man/showBedDataModel.Rd
pkgdown/assets/BED.html
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day01/Human-Genes-Ensembl-Entrez-100.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day01/Human-Genes-Ensembl-Entrez-20000.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day01/Mouse-Affy-Peptide-Ensembl-100.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day01/Mouse-Affy-Peptide-Ensembl-20000.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day01/Mouse-Peptides-Uniprot-Transcript-Ensembl-100.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day01/Mouse-Peptides-Uniprot-Transcript-Ensembl-20000.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day02/Human-Genes-Ensembl-Entrez-100.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day02/Human-Genes-Ensembl-Entrez-20000.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day02/Mouse-Affy-Peptide-Ensembl-100.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day02/Mouse-Affy-Peptide-Ensembl-20000.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day02/Mouse-Peptides-Uniprot-Transcript-Ensembl-100.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day02/Mouse-Peptides-Uniprot-Transcript-Ensembl-20000.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day03/Human-Genes-Ensembl-Entrez-100.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day03/Human-Genes-Ensembl-Entrez-20000.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day03/Mouse-Affy-Peptide-Ensembl-100.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day03/Mouse-Affy-Peptide-Ensembl-20000.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day03/Mouse-Peptides-Uniprot-Transcript-Ensembl-100.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day03/Mouse-Peptides-Uniprot-Transcript-Ensembl-20000.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day04/Human-Genes-Ensembl-Entrez-100.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day04/Human-Genes-Ensembl-Entrez-20000.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day04/Mouse-Affy-Peptide-Ensembl-100.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day04/Mouse-Affy-Peptide-Ensembl-20000.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day04/Mouse-Peptides-Uniprot-Transcript-Ensembl-100.rda
supp/BED-F1000-Article-V2/Analyses/Perf-Results/Day04/Mouse-Peptides-Uniprot-Transcript-Ensembl-20000.rda
supp/BED-F1000-Article-V2/Analyses/S01-gff-processing.R
supp/BED-F1000-Article-V2/Analyses/S02-Datasets.R
supp/BED-F1000-Article-V2/Analyses/S03-Performance.R
supp/BED-F1000-Article-V2/BED-F1000-Article.Rmd
supp/BED-F1000-Article-V2/BED-F1000-Article.pdf
supp/BED-F1000-Article-V2/BED-F1000-Article.tex
supp/BED-F1000-Article-V2/BED-F1000-Article_files/figure-latex/beidTables-1.pdf
supp/BED-F1000-Article-V2/BED-F1000-Article_files/figure-latex/geneLocations-1.pdf
supp/BED-F1000-Article-V2/BED-F1000-Article_files/figure-latex/perf-1.pdf
supp/BED-F1000-Article-V2/BED-F1000-Article_files/figure-latex/vennTools-1.pdf
supp/BED-F1000-Article-V2/BED-References.bib
supp/BED-F1000-Article-V2/F1000header.png
supp/BED-F1000-Article-V2/f1000_styles.sty
supp/BED-F1000-Article-V2/img/BED-Data-Model.pdf
supp/BED-F1000-Article-V2/img/ILMN_1220595-Conversion.png
supp/BED-F1000-Article-V2/img/MAPT-Identifiers.png
supp/BED-F1000-Article-V2/img/TAS2R8-Identifiers.png
supp/BED-F1000-Article-V2/img/findBe.png
supp/BED-F1000-Article/BED-F1000-Article.Rmd
supp/BED-F1000-Article/BED-F1000-Article.log
supp/BED-F1000-Article/BED-F1000-Article.pdf
supp/BED-F1000-Article/BED-F1000-Article.tex
supp/BED-F1000-Article/BED-F1000-Article_files/figure-latex/beidTables-1.pdf
supp/BED-F1000-Article/BED-F1000-Article_files/figure-latex/plot-1.pdf
supp/BED-F1000-Article/BED-F1000-Article_files/figure-latex/vennTools-1.pdf
supp/BED-F1000-Article/BED-References.bib
supp/BED-F1000-Article/F1000header.png
supp/BED-F1000-Article/f1000_styles.sty
supp/BED-F1000-Article/img/BED-Data-Model.pdf
supp/BED-F1000-Article/img/ILMN_1220595-Conversion.png
supp/BED-F1000-Article/img/MAPT-Identifiers.png
supp/BED-F1000-Article/img/TAS2R8-Identifiers.png
supp/BED-F1000-Article/img/findBe.png
supp/BED-R-Functions/BED-Functions-graph.R
supp/Build/Genodesy-instance/Rebuild-BED.Rmd
supp/Build/Genodesy-instance/Rebuild-BED.html
supp/Build/Genodesy-instance/Rebuild-BED.md
supp/Build/Genodesy-instance/build_config.json
supp/Build/Genodesy-instance/deploy_config.json
supp/Build/Genodesy-instance/prepare-files.R
supp/Build/README.md
supp/Build/S00-Prepare-large-files.sh
supp/Build/S01-NewBED-Container.sh
supp/Build/S02-Rebuild-BED.sh
supp/Build/S03-Dump-BED.sh
supp/Build/S11-Push-on-Zenodo.sh
supp/Build/S21-Deploy-from-Zenodo.sh
supp/Build/UCB-instance/Rebuild-BED.Rmd
supp/Build/UCB-instance/build_config.json
supp/Build/UCB-instance/helpers/loadMBObjects.R
supp/Build/UCB-instance/helpers/loadMBObjects_fromTKCat.R
supp/Build/UCB-instance/prepare-files.R
supp/Build/helpers/zenodo_upload.sh
supp/Build/neo4j-v3/Internal-instance/S01-NewIntBED-Container.sh
supp/Build/neo4j-v3/Internal-instance/S11-1-NewIntBED-Image.sh
supp/Build/neo4j-v3/Internal-instance/S11-2-NewIntBED-Archive.sh
supp/Build/neo4j-v3/Internal-instance/S12-IntBED-Container.sh
supp/Build/neo4j-v3/S03-NewBED-Image.sh
supp/Build/neo4j-v3/S04-Push-on-docker-hub.sh
supp/Build/neo4j-v3/S05-BED-Container.sh
supp/Build/requirements/R-packages.R
supp/Build/requirements/ubuntu-22.04-instance.sh
supp/S01-CRAN-Build.R
supp/logo/BED.png
supp/logo/BED.svg
supp/logo/cell-grey-blue.svg
supp/logo/cell-svgrepo-com.svg
supp/logo/id-bubbles.svg
vignettes/BED.Rmd
vignettes/img/BED-data-model.png
vignettes/img/BED.png
