API for AnnotationForge
Code for Building Annotation Database Packages

Global functions
AnnDbPkgSeed Man page
AnnDbPkgSeed-class Man page
NEW_makeOrgPackageFromNCBI Source code
OLD_makeOrgPackageFromNCBI Source code
addEssentialMetadata Source code
addMapCounts Source code
addMapMeta Source code
addMapMetadata Source code
addMeta Source code
addMetadata Source code
addOntologyData 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
asV 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
checkRetrieveNode Source code
class:AnnDbPkgSeed Man page
cleanRefSeqs Source code
cleanSrcMap 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
createTEMPNCBIBaseTable 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
filterManPages Source code
g.species Source code
generate.schema Source code
generateCols Source code
generateOrgDbName Source code
generateSeqnames.db Man page Source code
generateTempTableINSERTStatement 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
getDataAndAddToDb Source code
getEnsemblData Source code
getEntrezGenesFromTaxId Source code
getFastaSpeciesDirs Source code
getFiles Source code
getGODate Source code
getGOInfo Source code
getGeneStuff Source code
getMapForArabidopsisChipPkg Source code
getMapForBiocChipPkg Source code
getMapForOtherChipPkg Source code
getMapForYeastChipPkg Source code
getNCBIDateStamp Source code
getOrgDepFromMetadata Source code
getOrgSchema Source code
getOtherSrcDocs Source code
getProbeDataAffy Man page Source code
getProbeData_1lq Man page Source code
getSubDirs Source code
getSubNodeInfo Source code
getSymbolValuesForManPages Source code
initComputedSlots Source code
initWithDbDoc Source code
initWithDbMetada Source code
labelDuplicatedProbes Source code
lgExtraParanoia Source code
listMappings Source code
loadAnnDbPkgIndex Man page Source code
lookupTableName Source code
makeARABIDOPSISCHIP_DB Source code
makeAnnDbPkg Man page Source code
makeAnnDbPkg,AnnDbPkgSeed-method Man page
makeAnnDbPkg,character-method Man page
makeAnnDbPkg,list-method Man page
makeAnnDbPkgList Source code
makeAnnDbPkgs Source code
makeBOVINECHIP_DB Source code
makeBaseDBFromDLs Source code
makeBaseMaps Source code
makeBasePackage Source code
makeBasicMetadata Source code
makeCANINECHIP_DB Source code
makeCHICKENCHIP_DB Source code
makeCentralTable Source code
makeChipDbFromDataFrame Source code
makeChipPackage Man page Source code
makeDBPackage Man page Source code
makeECOLICHIP_DB Source code
makeEmptySimpleTable Source code
makeFLYCHIP_DB Source code
makeFooPkg Source code
makeGOTablesFromNCBI Source code
makeGenesTable Source code
makeHUMANCHIP_DB Source code
makeIndex Source code
makeInpDb Man page Source code
makeLegacyProbesTable Source code
makeMOUSECHIP_DB Source code
makeNewGOTables Source code
makeOrgDB Source code
makeOrgDbFromDataFrames Source code
makeOrgDbFromNCBI Source code
makeOrgPackage Man page Source code Source code
makeOrgPackageFromNCBI Man page Source code
makePIGCHIP_DB Source code
makeProbePackage Man page 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
makeUniversalMapping 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
ndexTaxIds Source code
padGOIds 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
popInpTable 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
populateBaseTable Source code
populateDB Man page Source code
prepareData Source code
prepareDataFromNCBI Source code
primaryFiles Source code
printOutBaseMaps Source code
probe2gene Source code
procDat Source code
regenDb Source code
removeCommentsFromFile Source code
rename Source code
sNCBICurrentWith Source code
sNCBIPopulatedWith Source code
sSingleString Source code
sSingleStringOrNA Source code
sSingleStringOrNull Source code
scrubAffyFileComments Source code
setNCBIDateStamp Source code
setupBaseDBFromDLs Source code
splitBy Source code
supportedNCBItypes Source code
test Source code
testForMultiples Source code
tossHyphens Source code
tryDL Source code
tryDL2 Source code
tweakMapName Source code
unwindGOs Source code
wrapBaseDBPackages Man page Source code
writeTable Source code
writeToNCBIDB Source code
writeToNCBIDB2 Source code
AnnotationForge documentation built on Nov. 17, 2017, 9:12 a.m.