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


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Documentation for package ‘IsoformSwitchAnalyzeR’ version 2.2.0

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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