API for AnnotationForge
Tools for building SQLite-based annotation data packages

Global functions
.addEssentialMetadata Source code
.addMapCounts Source code
.addMapMeta Source code
.addMapMetadata Source code
.addMeta Source code
.addMetadata Source code
.addOntologyData Source code
.asV Source code
.checkRetrieveNode Source code
.cleanupFiles Source code
.cloneMapMetadata Source code
.combineTwoLists Source code
.computeSimpleEGMapCounts Source code
.computeSimpleMapCounts Source code
.convertNullToNA Source code
.createAnnotPackage Source code
.createMetadataTables Source code
.doWeNeedUnigene Source code
.downloadAndPopulateAltGOData Source code
.downloadAndSaveToTemp Source code
.downloadData Source code
.dropOldTables Source code
.emptyGoFrame Source code
.ensemblMapsToEntrezId Source code
.expandGOFrame Source code
.extract Source code
.filterGOFrame Source code
.generateOrgDbName Source code
.getAFileSet Source code
.getAllEnrezGeneIdsFromNCBI Source code
.getAltGOData Source code
.getBlast2GO Source code
.getBlast2GOData Source code
.getChipCentralID Source code
.getChipSchema Source code
.getDBTag Source code
.getEnsemblData Source code
.getFiles Source code
.getGODate Source code
.getNCBIDateStamp Source code
.getOrgDepFromMetadata Source code
.getOrgSchema Source code
.getOtherSrcDocs Source code
.getSubDirs Source code
.getSubNodeInfo Source code
.indexTaxIds Source code
.isNCBICurrentWith Source code
.isNCBIPopulatedWith Source code
.isSingleString Source code
.isSingleStringOrNA Source code
.isSingleStringOrNull Source code
.lookupTableName Source code
.makeARABIDOPSISCHIP_DB Source code
.makeAnnDbPkg Source code
.makeAnnDbPkgList Source code
.makeAnnDbPkgs Source code
.makeBOVINECHIP_DB Source code
.makeBaseDBFromDLs Source code
.makeBasicMetadata Source code
.makeCANINECHIP_DB Source code
.makeCHICKENCHIP_DB Source code
.makeCentralTable Source code
.makeECOLICHIP_DB Source code
.makeEmptySimpleTable Source code
.makeFLYCHIP_DB Source code
.makeGOTablesFromNCBI Source code
.makeGenesTable Source code
.makeHUMANCHIP_DB Source code
.makeIndex Source code
.makeLegacyProbesTable Source code
.makeMOUSECHIP_DB Source code
.makeNewGOTables Source code
.makeOrgDB Source code
.makeOrgPackage Source code
.makePIGCHIP_DB Source code
.makeProbesTable Source code
.makeRATCHIP_DB Source code
.makeRHESUSCHIP_DB Source code
.makeSimpleDF Source code
.makeSimpleTable Source code
.makeTable Source code
.makeUnWoundGOTables Source code
.makeWORMCHIP_DB Source code
.makeXENOPUSCHIP_DB Source code
.makeYEASTCHIP_DB Source code
.makeZEBRAFISHCHIP_DB Source code
.mergeAndCleanAccession Source code
.mergeLists Source code
.mkGIdQ Source code
.modifyGOs Source code
.padGOIds Source code
.popInpTable Source code
.populateBaseTable Source code
.prepareData Source code
.primaryFiles Source code
.procDat Source code
.rename Source code
.setNCBIDateStamp Source code
.setupBaseDBFromDLs Source code
.test Source code
.testForMultiples Source code
.tossHyphens Source code
.tryDL Source code
.tryDL2 Source code
.tweakMapName Source code
.unwindGOs Source code
.writeToNCBIDB Source code
.writeToNCBIDB2 Source code
AnnDbPkgSeed Man page
AnnDbPkgSeed-class Man page
NEW_makeOrgPackageFromNCBI Source code
OLD_makeOrgPackageFromNCBI Source code
analyzeVacuumDisconnect Source code
appendAccessions Source code
appendAlias Source code
appendAraCyc Source code
appendAraCycEnzyme Source code
appendArabidopsisEntrezGenes Source code
appendArabidopsisGeneInfo Source code
appendArabidopsisGenes Source code
appendArabidopsisProbes Source code
appendChrlengths Source code
appendChromosomes Source code
appendChromsomeLocs Source code
appendCytogenicLocs Source code
appendEC Source code
appendEnsembl Source code
appendEnsembl2NCBI Source code
appendEnsemblProt Source code
appendEnsemblTrans Source code
appendFlyBase Source code
appendFlyBaseCG Source code
appendFlyBaseProt Source code
appendGO Source code
appendGOALL Source code
appendGeneInfo Source code
appendGenes Source code
appendKEGG Source code
appendMGI Source code
appendNCBI2Ensembl Source code
appendOmim Source code
appendPfam Source code
appendPreMeta Source code
appendProbes Source code
appendProsite Source code
appendPubmed Source code
appendRefseq Source code
appendUnigene Source code
appendYeastAlias Source code
appendYeastChromosomeFeatures Source code
appendYeastInterpro Source code
appendYeastOrphanMeta Source code
appendYeastPfam Source code
appendYeastProbes Source code
appendYeastSGD Source code
appendYeastSmart Source code
available.FastaEnsemblSpecies Source code
available.chipdbschemas Man page Source code
available.db0pkgs Man page Source code
available.dbschemas Man page Source code
available.ensembl.datasets Source code
buildEntrezGeneDbFromWebServices Source code
class:AnnDbPkgSeed Man page
cleanRefSeqs Source code
cleanSrcMap Source code
filterManPages Source code
g.species Source code
generate.schema Source code
generateSeqnames.db Man page Source code
getDataAndAddToDb Source code
getEntrezGenesFromTaxId Source code
getFastaSpeciesDirs Source code
getGOInfo Source code
getGeneStuff Source code
getMapForArabidopsisChipPkg Source code
getMapForBiocChipPkg Source code
getMapForOtherChipPkg Source code
getMapForYeastChipPkg Source code
getProbeDataAffy Man page Source code
getProbeData_1lq Man page Source code
getSymbolValuesForManPages Source code
initComputedSlots Source code
initWithDbDoc Source code
initWithDbMetada Source code
labelDuplicatedProbes Source code
listMappings Source code
loadAnnDbPkgIndex Man page Source code
makeAnnDbPkg Man page
makeAnnDbPkg,AnnDbPkgSeed-method Man page
makeAnnDbPkg,character-method Man page
makeAnnDbPkg,list-method Man page
makeBaseMaps Source code
makeBasePackage Source code
makeChipDbFromDataFrame Source code
makeChipPackage Man page Source code
makeDBPackage Man page Source code
makeFooPkg Source code
makeInpDb Man page Source code
makeOrgDbFromDataFrames Source code
makeOrgDbFromNCBI Source code
makeOrgPackage Man page Source code
makeOrgPackageFromNCBI Man page Source code
makeProbePackage Man page Source code
makeUniversalMapping Source code
popANOPHELESDB Source code
popARABIDOPSISCHIPDB Source code
popARABIDOPSISDB Source code
popBOVINECHIPDB Man page Source code
popBOVINEDB Man page Source code
popCANINECHIPDB Man page Source code
popCANINEDB Man page Source code
popCHICKENCHIPDB Man page Source code
popCHICKENDB Man page Source code
popCHIMPDB Source code
popECOLICHIPDB Man page Source code
popECOLIDB Man page Source code
popFLYCHIPDB Man page Source code
popFLYDB Man page Source code
popHUMANCHIPDB Man page Source code
popHUMANDB Man page Source code
popMALARIADB Man page Source code
popMOUSECHIPDB Man page Source code
popMOUSEDB Man page Source code
popPIGCHIPDB Man page Source code
popPIGDB Man page Source code
popRATCHIPDB Man page Source code
popRATDB Man page Source code
popRHESUSCHIPDB Source code
popRHESUSDB Source code
popWORMCHIPDB Man page Source code
popWORMDB Man page Source code
popXENOPUSCHIPDB Source code
popXENOPUSDB Source code
popYEASTCHIPDB Source code
popYEASTDB Man page Source code
popYEASTNCBIDB Man page Source code
popZEBRAFISHCHIPDB Man page Source code
popZEBRAFISHDB Man page Source code
populateDB Man page Source code
prepareDataFromNCBI Source code
printOutBaseMaps Source code
probe2gene Source code
regenDb Source code
removeCommentsFromFile Source code
scrubAffyFileComments Source code
splitBy Source code
supportedNCBItypes Source code
wrapBaseDBPackages Man page
writeTable Source code
AnnotationForge documentation built on May 2, 2020, 2 a.m.