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| analyzeAlternativeSplicing | Analyse alternative splicing (including intron retention(s)) |
| analyzeCPAT | Import Result of External Sequence Analysis |
| analyzeIntronRetention | Analyse alternative splicing (including intron retention(s)) |
| analyzeORF | Predictiction of Transcript Open Reading Frame. |
| analyzePFAM | Import Result of PFAM analysis |
| analyzeSignalP | Import Result of SignalP Analysis |
| analyzeSwitchConsequences | Analyze Consequences of Isoform Switches |
| CDSSet | Container for coding sequence (CDS) annotation information |
| CDSSet-class | Container for coding sequence (CDS) annotation information |
| createSwitchAnalyzeRlist | Create a switchAnalyzeRlist Object |
| exampleSwitchList | Example data for IsoformSwitchAnalyzeR |
| exampleSwitchListAnalyzed | Example data for IsoformSwitchAnalyzeR |
| exampleSwitchListIntermediary | Example data for IsoformSwitchAnalyzeR |
| extractCalibrationStatus | Extract Whether P-values were Corrected. |
| extractConsequenceEnrichment | Analyze data for enrichment of specific consequences |
| extractConsequenceEnrichmentComparison | Compare enrichment of specific consequences between comparisons |
| extractConsequenceGenomeWide | Genome wide Analysis of Consequences due to isoform switching |
| extractConsequenceSummary | Analyze Switch Consequences |
| extractExpressionMatrix | Extract Gene/Isoform Expression Matrix. |
| extractGenomeWideAnalysis | Genome wide Analysis of Consequences due to isoform switching |
| extractSequence | Extract nucloetide (and amino acid) sequence of transcripts. |
| extractSplicingEnrichment | Analyze data for enrichment of specific type of alternative splicing |
| extractSplicingEnrichmentComparison | Compare enrichment of specific type of alternative splicing between comparisons |
| extractSplicingGenomeWide | Genome wide Analysis of alternative splicing |
| extractSplicingSummary | Exracts alternative splicing summary |
| extractSwitchOverlap | Visualize Switch Overlap |
| extractSwitchSummary | Summarize Isoform Switches test Result. |
| extractTopSwitches | Extract Top Isoform Switches. |
| getCDS | Retrieve CDS information from UCSC |
| importCufflinksCummeRbund | Import CuffDiff (Cufflinks) Data Into R |
| importCufflinksFiles | Import CuffDiff (Cufflinks) Data Into R |
| importGTF | Import Transcripts from a GTF file into R |
| importIsoformExpression | Import expression data from Kallisto, Salmon or RSEM into R. |
| importRdata | Create SwitchAnalyzeRlist From Standard R Objects |
| isoformSwitchAnalysisCombined | Isoform Switch Analysis Workflow: Extract, Annoate and Visualize all Significant Isoform Swtiches |
| isoformSwitchAnalysisPart1 | Isoform Switch Analysis Workflow Part 1: Extract Isoform Switches and Their Sequences |
| isoformSwitchAnalysisPart2 | Isoform Switch Analysis Workflow Part 2: Plot All Isoform Switches and Their Annotation |
| isoformSwitchTest | Statistical Test of Isoform Switching. |
| isoformSwitchTestDRIMSeq | Statistical Test for identifying Isoform Switching via DRIMSeq. |
| isoformToGeneExp | Summarize isoform expression to gene level expression. |
| preFilter | Filtering of a switchAnalyzeRlist |
| prepareCuffExample | Prepare the Cufflinks example data |
| subsetSwitchAnalyzeRlist | A function which subset all enteries in a switchAnalyzeRlist. |
| switchAnalyzeRlist | Create a switchAnalyzeRlist Object |
| switchAnalyzeRlist-class | Create a switchAnalyzeRlist Object |
| switchPlot | Isoform Switch Analysis Plot |
| switchPlotGeneExp | Plots for Analyzing Expression and Isoform Usage |
| switchPlotIsoExp | Plots for Analyzing Expression and Isoform Usage |
| switchPlotIsoUsage | Plots for Analyzing Expression and Isoform Usage |
| switchPlotTopSwitches | Creating the Isoform Switch Analysis Plot for the Top Switches |
| switchPlotTranscript | Plot Transcript Structure and Annoation |