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 |
