An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)


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Documentation for package ‘IsoformSwitchAnalyzeR’ version 1.0.0

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analyzeCPAT Import Result of External Sequence Analysis
analyzeIntronRetention Detection of Intron Retion(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
createSwitchAnalyzeRlist Create a switchAnalyzeRlist Object
exampleSwitchList Example data for IsoformSwitchAnalyzeR
exampleSwitchListAnalyzed Example data for IsoformSwitchAnalyzeR
exampleSwitchListIntermediary Example data for IsoformSwitchAnalyzeR
extractCalibrationStatus Extract Whether P-values were Corrected.
extractConsequenceSummary Analyze Switch Consequences
extractExpressionMatrix Extract Gene/Isoform Expression Matrix.
extractGenomeWideAnalysis Genome wide Analysis of Changes in Isoform Features
extractSequence Extract nucloetide (and amino acid) sequence of transcripts.
extractSwitchSummary Summarize Isoform Switches test Result.
extractTopSwitches Extract Top Isoform Switches.
importCufflinksCummeRbund Import CuffDiff (Cufflinks) Data Into R
importCufflinksFiles Import CuffDiff (Cufflinks) Data Into R
importGTF Import Transcripts from a GTF file into R
importIsoformExpression Import expression data from Kallisto, Salmon or RSEM 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
isoformSwitchTest Statistical Test of Isoform Switching.
isoformSwitchTestDRIMSeq Statistical Test for identifying Isoform Switching via DRIMSeq.
isoformToGeneExp Summarize isoform expression to gene level expression.
preFilter Filtering of a switchAnalyzeRlist
prepareCuffExample Prepare the Cufflinks example data
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