API for IsoformSwitchAnalyzeR
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
| Global functions | |
|---|---|
| CDSSet | Man page Source code |
| CDSSet-class | Man page |
| allPairwiseFeatures | Source code |
| analyseCds | Source code |
| analyzeAlternativeSplicing | Man page Source code |
| analyzeCPAT | Man page Source code |
| analyzeCPC2 | Man page Source code |
| analyzeIUPred2A | Man page Source code |
| analyzeIntronRetention | Man page Source code |
| analyzeNetSurfP2 | Man page Source code |
| analyzeORF | Man page Source code |
| analyzeORFforPTC | Source code |
| analyzePFAM | Man page Source code |
| analyzeSignalP | Man page Source code |
| analyzeSwitchConsequences | Man page Source code |
| compareAnnotationOfTwoIsoforms | Source code |
| convertCoordinatsTranscriptToGenomic | Source code |
| createSwitchAnalyzeRlist | Man page Source code |
| cutGRanges | Source code |
| determineTranscriptClass | Source code |
| dim.switchAnalyzeRlist | Source code |
| estimateDifferentialRange | Source code |
| evalSig | Source code |
| exampleSwitchList | Man page |
| exampleSwitchListAnalyzed | Man page |
| exampleSwitchListIntermediary | Man page |
| expressionAnalysisPlot | Source code |
| extractConsequenceEnrichment | Man page Source code |
| extractConsequenceEnrichmentComparison | Man page Source code |
| extractConsequenceGenomeWide | Man page Source code |
| extractConsequenceSummary | Man page Source code |
| extractGeneExpression | Man page Source code |
| extractGenomeWideAnalysis | Man page Source code |
| extractSequence | Man page Source code |
| extractSigData | Source code |
| extractSplicingEnrichment | Man page Source code |
| extractSplicingEnrichmentComparison | Man page Source code |
| extractSplicingGenomeWide | Man page Source code |
| extractSplicingSummary | Man page Source code |
| extractSwitchOverlap | Man page Source code |
| extractSwitchPairs | Source code |
| extractSwitchSummary | Man page Source code |
| extractTopSwitches | Man page Source code |
| fixNames | Source code |
| getCDS | Man page Source code |
| grangesFracOverlap | Source code |
| head.switchAnalyzeRlist | Source code |
| importCufflinksFiles | Man page Source code |
| importGTF | Man page Source code |
| importIsoformExpression | Man page Source code |
| importRdata | Man page Source code |
| importSalmonData | Man page Source code |
| isoformSwitchAnalysisCombined | Man page Source code |
| isoformSwitchAnalysisPart1 | Man page Source code |
| isoformSwitchAnalysisPart2 | Man page Source code |
| isoformSwitchTestDEXSeq | Man page Source code |
| isoformSwitchTestDRIMSeq | Man page Source code |
| isoformToGeneExp | Man page Source code |
| isoformToIsoformFraction | Man page Source code |
| jaccardSimilarity | Source code |
| makeMinimumSwitchList | Source code |
| makeProperNames | Source code |
| medianQuartile | Source code |
| myAllFindORFsinSeq | Source code |
| myListToDf | Source code |
| ncol.switchAnalyzeRlist | Source code |
| newLineAtMiddel | Source code |
| nrow.switchAnalyzeRlist | Source code |
| preFilter | Man page Source code |
| prepareSalmonFileDataFrame | Man page Source code |
| show.switchAnalyzeRlist | Source code |
| startCapitalLetter | Source code |
| subsetSwitchAnalyzeRlist | Man page Source code |
| summary.switchAnalyzeRlist | Source code |
| switchAnalyzeRlist | Man page |
| switchAnalyzeRlist-class | Man page |
| switchPlot | Man page Source code |
| switchPlotGeneExp | Man page Source code |
| switchPlotIsoExp | Man page Source code |
| switchPlotIsoUsage | Man page Source code |
| switchPlotTopSwitches | Man page Source code |
| switchPlotTranscript | Man page Source code |
| tail.switchAnalyzeRlist | Source code |
| testFullRank | Source code |
| uniqueLength | Source code |
