DEXSeqIdsToGeneIds      Convert DEXSeq ids to gene ids
UTR2UTR53               Annotate UTRs from Gencode GTF as 5' or 3'
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
diffSplicingResults     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
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
readWhippetDIFFfiles    Read in a list of whippet .diff.gz files and
                        format as a data.frame
readWhippetDataSet      Import whippet results files as a
                        whippetDataSet
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
whippetDataSet-class    Class whippetDataSet
whippetTranscriptChangeSummary
                        Compare open reading frames for whippet
                        differentially spliced events
