analyzeAlternativSplicing | Analyse alternative splicing (including intron retention(s)) |
analyzeCPAT | Import Result of External Sequence Analysis |
analyzeCPC2 | Import Result of External Sequence Analysis |
analyzeIUPred2A | Import Result of IUPred2A analysis |
analyzeNetSurf2 | Import Result of NetSurfP2 analysis |
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 |
CDSSet | Container for coding sequence (CDS) annotation information |
expressionAnalysisPlots | Plots for Analyzing Expression and Isoform Usage |
extractConsequenceEnrichment | Analyze data for enrichment of specific consequences |
extractConsequenceEnrichmentComparison | Compare enrichment of specific consequences between... |
extractConsequenceSummary | Analyze Switch Consequences |
extractGeneExpression | Extract gene counts or abundances from a switchAnalyzeRlist... |
extractGenomeWideAnalysis | Genome wide Analysis of Consequences due to isoform switching |
extractGenomeWideSplicingAnalysis | Genome wide Analysis of alternative splicing |
extractSequence | Extract nucloetide (and amino acid) sequence of transcripts. |
extractSplicingEnrichment | Analyze data for enrichment of specific type of alternative... |
extractSplicingEnrichmentComparison | Compare enrichment of specific type of alternative splicing... |
extractSplicingSummary | Extracts alternative splicing summary |
extractSwitchOverlap | Visualize Switch Overlap |
extractSwitchSummary | Summarize Isoform Switches test Result. |
extractTopSwitches | Extract Top Isoform Switches. |
getCDS | Retrieve CDS information from UCSC |
importCufflinksGalaxyData | Import CuffDiff (Cufflinks) Data Into R |
importGTF | Import Transcripts from a GTF file into R |
importIsoformExpression | Import expression data from Kallisto, Salmon, RSEM or... |
importRdata | Create SwitchAnalyzeRlist From Standard R Objects |
importSalmonData | Direct creation of a switchAnalyzeRlist from Salmon... |
isoformSwitchAnalysisCombined | Isoform Switch Analysis Workflow: Extract, Annotate and... |
isoformSwitchAnalysisPart1 | Isoform Switch Analysis Workflow Part 1: Extract Isoform... |
isoformSwitchAnalysisPart2 | Isoform Switch Analysis Workflow Part 2: Plot All Isoform... |
IsoformSwitchTestDEXSeq | Statistical Test for identifying Isoform Switching via DEXSeq |
IsoformSwitchTestDRIMSeq | Statistical Test for identifying Isoform Switching via... |
isoformToGeneExp | Sum transcript/isoform expression to gene get level... |
isoformToIsoformFraction | Calculate isoform fraction from isoform abundance matrix |
preFilter | Filtering of a switchAnalyzeRlist |
prepareSalmonFilesDataFrame | Prepare data.frame needed run importSalmonData. |
subsetSwitchAnalyzeRlist | A function which subset all entries in a switchAnalyzeRlist. |
switchAnalyzeRlist | Create a switchAnalyzeRlist Object |
switchPlot | Isoform Switch Analysis Plot |
switchPlotTopSwitches | Creating the Isoform Switch Analysis Plot for the Top... |
switchPlotTranscript | Plot Transcript Structure and Annotation |
testData | Example data for IsoformSwitchAnalyzeR |
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