An R package to Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences (from RNA-seq data)


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Documentation for package ‘IsoformSwitchAnalyzeR’ version 1.4.0

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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
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
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
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
isoformSwitchTestDEXSeq Statistical Test for identifying Isoform Switching via DEXSeq
isoformSwitchTestDRIMSeq Statistical Test for identifying Isoform Switching via DRIMSeq.
isoformToGeneExp Summarize isoform expression to gene level expression.
isoformToIsoformFraction Calculate isoform fraction from isoform abundance matrix
preFilter Filtering of a switchAnalyzeRlist
removeAnnoationData Removes data not needed after switch identification.
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