Man pages for fursham-h/ponder
| classifyAltSegments | Classify alternative splicing features |
| classifyAS | Classify alternative splicing between transcripts |
| getBestRef | Title |
| getORFold | _ workflow: Test transcript for NMD feature against a... |
| gff3togtfconvert | GFF3 to GTF converter |
| indentifyAddedRemovedRegions | Identify regions that are specific to one of the two... |
| matchGeneIDs | Match Gene IDs from query GTF/GFF3 file |
| matchSeqLevels | Match seqnames of input GRanges to reference GRanges |
| old_resizeTranscripts | Resize GRanges transcript object |
| prepareAnalysis | NMDer workflow: Preparing for analysis |
| prepareInputs | NMDer workflow: Import files |
| prePonder | PONDER workflow: Prepare PONDER analysis |
| preTesting | NMDer workflow: Check and match input annotations |
| reconstructCDS | Reconstruct CDS with alternative internal and downstream... |
| reconstructCDSstart | Reconstruct CDS with alternate 5' exons |
| resizeGRangesTranscripts | Resize 5' and 3' ends of a transcript GenomicRanges |
| runMain | _ workflow: Test transcripts for NMD feature |
| runPonder | PONDER workflow: Run PONDER analysis |
| testNMD | Test ORF for NMD |
| testTXforStart | Test transcripts for annotated start codons |
