addORFfromGTF | Add CDS from a GTF file to a switchAnalyzeRlist. |
analyzeAlternativeSplicing | Analyse alternative splicing (including intron retention(s)) |
analyzeCPAT | Import Result of External Sequence Analysis |
analyzeCPC2 | Import Result of External Sequence Analysis |
analyzeDeepLoc2 | Import Result of DeepLoc2 Analysis |
analyzeDeepTMHMM | Import Result of a DeepTMHMM analysis |
analyzeIntronRetention | Analyse alternative splicing (including intron retention(s)) |
analyzeIUPred2A | Import Result of IUPred2A or IUPred3 analysis |
analyzeNetSurfP2 | Import Result of NetSurfP2 analysis |
analyzeNovelIsoformORF | Prediction of Isoform Open Reading Frames. |
analyzeORF | Prediction of Transcript Open Reading Frame. |
analyzePFAM | Import Result of PFAM analysis |
analyzeSignalP | Import Result of SignalP Analysis |
analyzeSwitchConsequences | Analyze Consequences of Isoform Switches |
createSwitchAnalyzeRlist | Create a switchAnalyzeRlist Object |
exampleSwitchList | Example data for IsoformSwitchAnalyzeR |
exampleSwitchListAnalyzed | Example data for IsoformSwitchAnalyzeR |
exampleSwitchListIntermediary | Example data for IsoformSwitchAnalyzeR |
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 |
extractGeneExpression | Extract raw gene counts or abundances from a switchAnalyzeRlist object. |
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 | Extracts alternative splicing summary |
extractSubCellShifts | Global overview of sub-cellular location changes |
extractSwitchOverlap | Visualize Switch Overlap |
extractSwitchSummary | Summarize Isoform Switches test Result. |
extractTopSwitches | Extract Top Isoform Switches. |
importCufflinksFiles | Import CuffDiff (Cufflinks) Data Into R |
importGTF | Import Transcripts from a GTF file into R |
importIsoformExpression | Import expression data from Kallisto, Salmon, RSEM or StringTie into R. |
importRdata | Create SwitchAnalyzeRlist From Standard R Objects |
importSalmonData | Direct creation of a switchAnalyzeRlist from Salmon quantification |
isoformSwitchAnalysisCombined | Isoform Switch Analysis Workflow: Extract, Annotate and Visualize all Significant Isoform Switches |
isoformSwitchAnalysisPart1 | Isoform Switch Analysis Workflow Part 1: Extract Isoform Switches and Their Bio-sequences |
isoformSwitchAnalysisPart2 | Isoform Switch Analysis Workflow Part 2: Plot All Isoform Switches and Their Annotation |
isoformSwitchTestDEXSeq | Statistical Test for identifying Isoform Switching via DEXSeq |
isoformSwitchTestSatuRn | Statistical Test for identifying Isoform Switching via satuRn. |
isoformToGeneExp | Sum transcript/isoform expression to gene get level expression. |
isoformToIsoformFraction | Calculate isoform fraction from isoform abundance matrix |
preFilter | Filtering of a switchAnalyzeRlist |
prepareSalmonFileDataFrame | Prepare data.frame needed run importSalmonData. |
subsetSwitchAnalyzeRlist | A function which subset all entries 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 Annotation |