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

analyzeAlternativSplicingAnalyse alternative splicing (including intron retention(s))
analyzeCPATImport Result of External Sequence Analysis
analyzeORFPredictiction of Transcript Open Reading Frame.
analyzePFAMImport Result of PFAM analysis
analyzeSignalPImport Result of SignalP Analysis
analyzeSwitchConsequencesAnalyze Consequences of Isoform Switches
CDSSetContainer for coding sequence (CDS) annotation information
expressionAnalysisPlotsPlots for Analyzing Expression and Isoform Usage
extractConsequenceEnrichmentAnalyze data for enrichment of specific consequences
extractConsequenceEnrichmentComparisonCompare enrichment of specific consequences between...
extractConsequenceSummaryAnalyze Switch Consequences
extractExpressionMatrixExtract Gene/Isoform Expression Matrix.
extractGenomeWideAnalysisGenome wide Analysis of Consequences due to isoform switching
extractGenomeWideSplicingAnalysisGenome wide Analysis of alternative splicing
extractSequenceExtract nucloetide (and amino acid) sequence of transcripts.
extractSplicingEnrichmentAnalyze data for enrichment of specific type of alternative...
extractSplicingEnrichmentComparisonCompare enrichment of specific type of alternative splicing...
extractSplicingSummaryExracts alternative splicing summary
extractSwitchOverlapVisualize Switch Overlap
extractSwitchSummarySummarize Isoform Switches test Result.
extractTopSwitchesExtract Top Isoform Switches.
getCDSRetrieve CDS information from UCSC
importCufflinksGalaxyDataImport CuffDiff (Cufflinks) Data Into R
importGTFImport Transcripts from a GTF file into R
importIsoformExpressionImport expression data from Kallisto, Salmon, RSEM or...
importRdataCreate SwitchAnalyzeRlist From Standard R Objects
isoformSwitchAnalysisCombinedIsoform Switch Analysis Workflow: Extract, Annoate and...
isoformSwitchAnalysisPart1Isoform Switch Analysis Workflow Part 1: Extract Isoform...
isoformSwitchAnalysisPart2Isoform Switch Analysis Workflow Part 2: Plot All Isoform...
IsoformSwitchTestDEXSeqStatistical Test for identifying Isoform Switching via DEXSeq
IsoformSwitchTestDRIMSeqStatistical Test for identifying Isoform Switching via...
isoformToGeneExpSummarize isoform expression to gene level expression.
isoformToIsoformFractionCalculate isoform fraction from isoform abundance matrix
preFilterFiltering of a switchAnalyzeRlist
removeAnnoationDataRemoves data not needed after switch identification.
subsetSwitchAnalyzeRlistA function which subset all enteries in a switchAnalyzeRlist.
switchAnalyzeRlistCreate a switchAnalyzeRlist Object
switchPlotIsoform Switch Analysis Plot
switchPlotTopSwitchesCreating the Isoform Switch Analysis Plot for the Top...
switchPlotTranscriptPlot Transcript Structure and Annoation
testDataExample data for IsoformSwitchAnalyzeR
IsoformSwitchAnalyzeR documentation built on Nov. 1, 2018, 3:38 a.m.