CDSSet                  Container for coding sequence (CDS) annotation
                        information
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
analyzeIUPred2A         Import Result of IUPred2A 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
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.
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
extractSwitchOverlap    Visualize Switch Overlap
extractSwitchSummary    Summarize Isoform Switches test Result.
extractTopSwitches      Extract Top Isoform Switches.
getCDS                  Retrieve CDS information from UCSC
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
isoformSwitchTestDRIMSeq
                        Statistical Test for identifying Isoform
                        Switching via DRIMSeq.
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.
switchPlot              Isoform Switch Analysis Plot
switchPlotGeneExp       Plots for Analyzing Expression and Isoform
                        Usage
switchPlotTopSwitches   Creating the Isoform Switch Analysis Plot for
                        the Top Switches
switchPlotTranscript    Plot Transcript Structure and Annotation
