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| addBroadTypes | Change transcript biotypes to a broader set |
| addIntronInTranscript | Add a retained intron to the transcripts it is skipped by |
| alternativeIntronUsage | Create transcripts with alternative intron usage |
| annotateGeneModel | Annotate a GRanges gene model with ORF boundries for visualisation with Gviz |
| attrChangeAltSpliced | Evaluate the change in an attribute between a set of 'normal' transcripts and 'alternative' transcripts |
| coordinates | Method coordinates |
| coordinates-method | Method coordinates |
| DEXSeqIdsToGeneIds | Convert DEXSeq ids to gene ids |
| diffSplicingResults | Method diffSplicingResults |
| diffSplicingResults-method | Method diffSplicingResults |
| exonsToTranscripts | Convert an exon-level gtf annotation to a transcript-level gtf annotation |
| filterGtfOverlap | Filter a GTF overlap to remove exons when exon is annotated as a CDS/UTR |
| filterWhippetEvents | Filter out significant events from a whippet diff comparison |
| findDEXexonType | Find a DEXSeq exons' biotype |
| findExonContainingTranscripts | Given the location of a whole spliced in exon, find transcripts which can splice out this exon |
| findIntronContainingTranscripts | Given the location of a whole retained intron, find transcripts which splice out this intron |
| findJunctionPairs | Find alternative junctions for Whippet alternative splicing events |
| formatWhippetEvents | Format Whippet co-ordinates as a GRanges object |
| getOrfs | Get open reading frames for transcripts |
| getUOrfs | Get upstream open reading frames for transcripts with annotated main ORFs |
| junctions | Method junctions |
| junctions-method | Method junctions |
| leafcutterTranscriptChangeSummary | Compare open reading frames for whippet differentially spliced events |
| makeGeneModel | Convert GRanges gene model to data.frame for visualisation with Gviz |
| maxLocation | Find the largest distance between two vectors of numbers Helper function for get_orfs |
| orfDiff | Evaluate changes to ORFs caused by alternative splicing |
| orfSimilarity | calculate percentage of orfB contained in orfA |
| overlapTypes | Annotate introns and exonic parts by overlaping exon biotype |
| readCounts | Method readCounts |
| readCounts-method | Method readCounts |
| readWhippetDataSet | Import whippet results files as a whippetDataSet |
| readWhippetDIFFfiles | Read in a list of whippet .diff.gz files and format as a data.frame |
| readWhippetJNCfiles | Read in a list of whippet .jnc.gz files and format as a GRanges object |
| readWhippetPSIfiles | Read in a list of whippet .psi.gz files and format as a data.frame |
| removeDuplicateTranscripts | Remove transcript duplicates |
| removeSameExon | Remove exon duplicates |
| removeVersion | Remove version number from ensembl gene/transcript ids |
| reorderExonNumbers | Reorder the exon numbers in a gtf annotation |
| replaceJunction | Find transcripts containing/overlapping junctions and replace them with alternative junctions |
| skipExonInTranscript | Remove and include a skipped exon from the transcripts it overlaps |
| summariseExonTypes | Summarise exon biotypes to broader categories |
| transcriptChangeSummary | Compare open reading frames for two sets of paired transcripts |
| UTR2UTR53 | Annotate UTRs from Gencode GTF as 5' or 3' |
| whippetDataSet-class | Class whippetDataSet |
| whippetTranscriptChangeSummary | Compare open reading frames for whippet differentially spliced events |