# Tools for spliced gene structure manipulation and analysis

## Documentation for package ‘GeneStructureTools’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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