API for pmoulos/sitadela
An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms

Global functions
.annotationExists Source code
.annotationTypeFromInputArgs Source code
.annotationWorker Source code
.browseContent Source code
.browseUserContent Source code
.bypassTimeoutByFilters Source code
.checkDbPath Source code
.checkEnsVer Source code
.checkIfBSgenomesInstalled Source code
.checkMainArgs Source code
.checkNumArgs Source code
.checkTextArgs Source code
.checkUTRPossible Source code
.checkUcscToEnsembl Source code
.chromInfoFromBAM Source code
.chromInfoFromSeqinfo Source code
.chromInfoToSeqInfoDf Source code
.chromInfoWrapperGID Source code
.collapseFailures Source code
.containsVersionedGT Source code
.defaultDbPath Source code
.dfOgr Source code
.dropAnnotation Source code
.formatFromGr Source code
.formatFromGrE Source code
.formatTxDb2Exon Source code
.getAttributes Source code
.getBiotypes Source code
.getDataset Source code
.getDefaultDbPath Source code
.getExonAttributes Source code
.getFilter Source code
.getGeneAttributes Source code
.getHost Source code
.getTranscriptAttributes Source code
.getTranscriptExonAttributes Source code
.getTranscriptUtrAttributes Source code
.getUcscCredentials Source code
.getUcscQuery Source code
.getUcscQueryNcbiExon Source code
.getUcscQueryNcbiGene Source code
.getUcscQueryNcbiTranscript Source code
.getUcscQueryRefseqExon Source code
.getUcscQueryRefseqGene Source code
.getUcscQueryRefseqTranscript Source code
.getUcscQueryUcscExon Source code
.getUcscQueryUcscGene Source code
.getUcscQueryUcscTranscript Source code
.getUcscRefseqVersionedUtrQuery Source code
.getUcscTabledef Source code
.getUcscTabledefNcbi Source code
.getUcscTabledefRefseq Source code
.getUcscTabledefUcsc Source code
.getUcscTblTpl Source code
.getUcscToEnsembl Source code
.getValidArgs Source code
.getValidChrs Source code
.getValidChrsWithMit Source code
.getVersionedExonAttributes Source code
.getVersionedFilter Source code
.getVersionedGeneAttributes Source code
.getVersionedTranscriptAttributes Source code
.getVersionedTranscriptExonAttributes Source code
.getVersionedTranscriptUtrAttributes Source code
.initTables Source code
.insertContent Source code
.installedVersions Source code
.loadAnnotationOnTheFly Source code
.loadPrebuiltAnnotation Source code
.localTblDef Source code
.makeAnnotationQuerySet Source code
.makeExonExonFromTxDb Source code
.makeGeneExonFromTxDb Source code
.makeGeneGeneFromTxDb Source code
.makeGeneUtrFromTxDb Source code
.makeIdMap Source code
.makeSumGeneExonFromTxDb Source code
.makeSumGeneUtrFromTxDb Source code
.makeSumTranscriptExonFromTxDb Source code
.makeSumTranscriptGeneFromTxDb Source code
.makeSumTranscriptUtrFromTxDb Source code
.makeTranscriptExonFromTxDb Source code
.makeTranscriptGeneFromTxDb Source code
.makeTranscriptUtrFromTxDb Source code
.makeUcscRefseqUtrTable Source code
.nameAnnotationFromMetaType Source code
.notUseMapEx Source code
.notUseMapUtr Source code
.onLoad Source code
.orgsWithNoVersion Source code
.orgsWithVersion Source code
.orgsWithVersionAfter90 Source code
.ucscToEnsembl Source code
.useMapEx Source code
.useMapTr Source code
.useMapUtrEx Source code
.validateDbCon Source code
.validateEnsemblVersions Source code
addAnnotation Man page Source code
addCustomAnnotation Man page Source code
annotationFromCustomGtf Source code
cmclapply Source code
correctTranscripts Source code
getAnnotation Man page Source code
getBsOrganism Source code
getChromInfo Source code
getDbPath Man page Source code
getEnsemblAnnotation Source code
getGcContent Source code
getInstalledAnnotations Man page Source code
getSeqInfo Man page Source code
getSupportedOrganisms Source code
getSupportedRefDbs Source code
getSupportedUcscDbs Source code
getUcscAnnotation Source code
getUcscDbl Source code
getUcscOrganism Source code
getUcscTableNameUtr Source code
getUcscUtr Source code
getUserAnnotations Man page Source code
importCustomAnnotation Man page Source code
importCustomGtf Source code
initDatabase Source code
loadAnnotation Man page Source code
loadBsGenome Source code
parseCustomGtf Source code
reduceExons Source code
reduceTranscripts Source code
reduceTranscriptsExons Source code
reduceTranscriptsUtr Source code
removeAnnotation Man page Source code
setDbPath Man page Source code
testCustomBuild Man page Source code
testCustomGtf Man page Source code
testEnsembl Man page Source code
testEnsemblSimple Man page Source code
testKnownBuild Man page Source code
testUcsc Man page Source code
testUcscAll Man page Source code
testUcscUtr Man page Source code
testUcscUtrAll Man page Source code
pmoulos/sitadela documentation built on May 19, 2024, 3:52 a.m.