Tools for spliced gene structure manipulation and analysis

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Documentation for package ‘GeneStructureTools’ version 1.29.0

• 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