# Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.

## Documentation for package ‘IsoformSwitchAnalyzeR’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
analyzeIntronRetention | Analyse alternative splicing (including intron retention(s))
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
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
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
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.
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