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 |
| .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 |
