API for customProDB
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
| Global functions | |
|---|---|
| .Ensembl.fetchAttribTypeIdForTopLevelSequence | Source code |
| .Ensembl.fetchChromLengthsFromCoreUrl | Source code |
| .Ensembl.fetchTopLevelSequenceIds | Source code |
| .Ensembl.getFtpUrlToMySQL | Source code |
| .Ensembl.getMySQLCoreDir | Source code |
| .Ensembl.getMySQLCoreUrl | Source code |
| .Ensembl.getTable | Source code |
| .Ensembl.getTable.seq_region | Source code |
| .Ensembl.listMySQLCoreDirs | Source code |
| .UCSC_dbselect | Source code |
| .dbFileConnect | Source code |
| .extractCdsRangesFromBiomartTable | Source code |
| .extractEnsemblReleaseFromDbVersion | Source code |
| .extractSpeciesFromDatasetDesc | Source code |
| .gen_splicmatrix | Source code |
| .getAllDatasetAttrGroups | Source code |
| .getBiomartDbVersion | Source code |
| .getDatasetAttrGroups | Source code |
| .lsFtpUrl | Source code |
| .makeBiomartChrominfo | Source code |
| .makeBiomartGenes | Source code |
| .makeBiomartSplicings | Source code |
| .makeBiomartTranscripts | Source code |
| .makeCdsDataFrameFromRanges | Source code |
| .map2trans | Source code |
| .normUtrCoords | Source code |
| .parseBMFiltersParams | Source code |
| .parseBMMartParams | Source code |
| .parseBMValuesParams | Source code |
| .prepareBiomartMetadata | Source code |
| Bed2Range | Man page Source code |
| InputVcf | Man page Source code |
| JunctionType | Man page Source code |
| Multiple_VCF | Man page Source code |
| OutputNovelJun | Man page Source code |
| OutputVarprocodingseq | Man page Source code |
| OutputVarproseq | Man page Source code |
| OutputVarproseq_single | Man page Source code |
| Outputaberrant | Man page Source code |
| Outputproseq | Man page Source code |
| OutputsharedPro | Man page Source code |
| Positionincoding | Man page Source code |
| PrepareAnnotationEnsembl | Man page Source code |
| PrepareAnnotationRefseq | Man page Source code |
| SharedJunc | Man page Source code |
| Varlocation | Man page Source code |
| aaVariation | Man page Source code |
| calculateRPKM | Man page Source code |
| dbEasyPreparedQuery | Source code |
| dbEasyQuery | Source code |
| debugSQL | Source code |
| easyRun | Man page Source code |
| easyRun_mul | Man page Source code |
| fetchChromLengthsFromEnsembl | Source code |
| getChromInfoFromBiomart | Source code |
| getMartAttribList | Source code |
| get_cached_dbconn | Source code |
| get_cached_dbfile | Source code |
| get_dbconn | Source code |
| get_dbfile | Source code |
| get_dbtable | Source code |
| hasCol | Source code |
| joinDataFrameWithName2Val | Source code |
| makeExonRankCol | Source code |
| makeIdsForUniqueDataFrameRows | Source code |
| makeTranscriptDbFromBiomart_archive | Source code |
| matchCircularity | Source code |
| scanMart | Source code |
| scanMarts | Source code |
| setDataFrameColClass | Source code |
