Man pages for betsig/GeneStructureTools
Tools for spliced gene structure manipulation and analysis
| addIntronInTranscript | Add a retained intron to the transcripts it is skipped by |
| addSets | Add set numbers to introns |
| alternativeIntronUsage | Create transcripts with alternative intron usage |
| alterTranscriptStartEnds | Find transcripts overlapping first/last exons and alter their... |
| altIntronRmats | Generate isoforms with and without a retain intron from RMATS... |
| altSpliceSiteRmats | Generate isoforms with different 5' or 3' splice site usage... |
| annotateEventCoords | annotate event coordinates with exon/transcript/gene ids. |
| annotateGeneModel | Annotate a GRanges gene model with ORF boundries for... |
| annotateOverlapRmats | Find overlaps from a rmats GRanges to reference exons and... |
| attrChangeAltSpliced | Evaluate the change in an attribute between a set of 'normal'... |
| betweenNumbers | Generate vector of integers between two numbers... |
| compareContains | compare two strings of concatenated sequence features |
| coordinates-methods | Method coordinates |
| cumsumANDpad | Cumulative sum of a sequence of numbers, padded with NA |
| diffSplicingResults-methods | Method diffSplicingResults |
| duplicateReference | Duplicate a reference Granges (exon-level) for each... |
| exonsToIntrons | Generate a introns Granges from an exons Granges |
| exonsToTranscripts | Convert an exon-level gtf annotation to a transcript-level... |
| extractEvent-methods | Method extractEvent |
| featureTypes | Evaluate changes to ORFs caused by alternative splicing |
| filterIrfEvents | Filter out significant events from a irfDataSet |
| filterRmatsEvents | Filter out significant events from a RMATS dataset |
| filterWhippetEvents | Filter out significant events from a whippet diff comparison |
| findExonContainingTranscripts | Given the location of a whole spliced in exon, find... |
| findIntronContainingTranscripts | Given the location of a whole retained intron, find... |
| findJunctionPairs | Find alternative junctions for Whippet alternative splicing... |
| findOverlaps.junc | Find overlaps where the start/end coordinates are the same |
| 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... |
| irfDataSet-class | Class irfDataSet |
| irfResults-methods | Method irfResults |
| irfTranscriptChangeSummary | Compare open reading frames for RMATS differentially spliced... |
| junctions-methods | Method junctions |
| leafcutterIntronsToExons | Create exon ranges from leafcutter intron ranges |
| leafcutterTranscriptChangeSummary | Compare open reading frames for whippet differentially... |
| makeGeneModel | Convert GRanges gene model to data.frame for visualisation... |
| makeNewLeafExons | Create new exon ranges for a cryptic splice junction |
| makeNewLeafExonsUnanchored | Create new exon ranges for a cryptic unachored splice... |
| matrix2combinations | Get a list of all potential range combinations, covering the... |
| maxLocation | Find the largest distance between two vectors of numbers... |
| orfDiff | Evaluate changes to ORFs caused by alternative splicing |
| orfSimilarity | calculate percentage of orfB contained in orfA |
| overlap2matrix | Create a 0/1 matrix from a Ranges overlap |
| readCounts-methods | Method readCounts |
| readIrfDataSet | Import IRFinder results files as a irfDataSet |
| readLeafcutterJunctions | Create junction ranges from STAR junction files |
| readRmatsDataSet | Import RMATS Turbo results files as a rmatsDataSet |
| readWhippetDataSet | Import whippet results files as a whippetDataSet |
| readWhippetDIFFfiles | Read in a list of whippet .diff.gz files and format as a... |
| readWhippetJNCfiles | Read in a list of whippet .jnc.gz files and format as a... |
| readWhippetPSIfiles | Read in a list of whippet .psi.gz files and format as a... |
| reformatExons | reformat a exons GRanges with first/last annotations and... |
| removeDuplicatePairs | remove any duplicate pairs of events/reference transcripts... |
| removeDuplicateTranscripts | Remove transcript duplicates |
| removeExonsBetween | Remove any exons in a transcript within an event range |
| 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... |
| rmatsDataSet-class | Class rmatsDataSet |
| rmatsTranscriptChangeSummary | Compare open reading frames for RMATS differentially spliced... |
| skipExonByJunction | Generate isoforms with and without a skipped exon (or... |
| skipExonInTranscript | Remove and include a skipped exon from the transcripts it... |
| splitLongExons | Split long exons in two if they overlap an event |
| transcriptChangeSummary | Compare open reading frames for two sets of paired... |
| UTR2UTR53 | Annotate UTRs from Gencode GTF as 5' or 3' |
| whippetDataSet-class | Class whippetDataSet |
| whippetTranscriptChangeSummary | Compare open reading frames for whippet differentially... |
