Man pages for betsig/GeneStructureTools
Tools for spliced gene structure manipulation and analysis

addBroadTypesChange transcript biotypes to a broader set
addIntronInTranscriptAdd a retained intron to the transcripts it is skipped by
addSetsAdd set numbers to introns
alternativeIntronUsageCreate transcripts with alternative intron usage
annotateGeneModelAnnotate a GRanges gene model with ORF boundries for...
attrChangeAltSplicedEvaluate the change in an attribute between a set of 'normal'...
compareContainscompare two strings of concatenated sequence features
coordinates-methodsMethod coordinates
cumsumANDpadCumulative sum of a sequence of numbers, padded with NA
DEXSeqIdsToGeneIdsConvert DEXSeq ids to gene ids
diffSplicingResults-methodsMethod diffSplicingResults
exonsToTranscriptsConvert an exon-level gtf annotation to a transcript-level...
featureTypesEvaluate changes to ORFs caused by alternative splicing
filterGtfOverlapFilter a GTF overlap to remove exons when exon is annotated...
filterWhippetEventsFilter out significant events from a whippet diff comparison
findDEXexonTypeFind a DEXSeq exons' biotype
findExonContainingTranscriptsGiven the location of a whole spliced in exon, find...
findIntronContainingTranscriptsGiven the location of a whole retained intron, find...
findJunctionPairsFind alternative junctions for Whippet alternative splicing...
formatWhippetEventsFormat Whippet co-ordinates as a GRanges object
getOrfsGet open reading frames for transcripts
getUOrfsGet upstream open reading frames for transcripts with...
junctions-methodsMethod junctions
leafcutterIntronsToExonsCreate exon ranges from leafcutter intron ranges
leafcutterTranscriptChangeSummaryCompare open reading frames for whippet differentially...
makeGeneModelConvert GRanges gene model to data.frame for visualisation...
makeNewLeafExonsCreate new exon ranges for a cryptic splice junction
makeNewLeafExonsUnanchoredCreate new exon ranges for a cryptic unachored splice...
matrix2combinationsGet a list of all potential range combinations, covering the...
maxLocationFind the largest distance between two vectors of numbers...
orfDiffEvaluate changes to ORFs caused by alternative splicing
orfSimilaritycalculate percentage of orfB contained in orfA
overlap2matrixCreate a 0/1 matrix from a Ranges overlap
overlapTypesAnnotate introns and exonic parts by overlaping exon biotype
readCounts-methodsMethod readCounts
readLeafcutterJunctionsCreate junction ranges from STAR junction files
readWhippetDataSetImport whippet results files as a whippetDataSet
readWhippetDIFFfilesRead in a list of whippet .diff.gz files and format as a...
readWhippetJNCfilesRead in a list of whippet .jnc.gz files and format as a...
readWhippetPSIfilesRead in a list of whippet .psi.gz files and format as a...
removeDuplicateTranscriptsRemove transcript duplicates
removeSameExonRemove exon duplicates
removeVersionRemove version number from ensembl gene/transcript ids
reorderExonNumbersReorder the exon numbers in a gtf annotation
replaceJunctionFind transcripts containing/overlapping junctions and replace...
skipExonInTranscriptRemove and include a skipped exon from the transcripts it...
summariseExonTypesSummarise exon biotypes to broader categories
transcriptChangeSummaryCompare open reading frames for two sets of paired...
UTR2UTR53Annotate UTRs from Gencode GTF as 5' or 3'
whippetDataSet-classClass whippetDataSet
whippetTranscriptChangeSummaryCompare open reading frames for whippet differentially...
betsig/GeneStructureTools documentation built on Oct. 25, 2018, 2:11 p.m.