Man pages for kvittingseerup/IsoformSwitchAnalyzeR
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.

addORFfromGTFAdd CDS from a GTF file to a switchAnalyzeRlist.
analyzeAlternativSplicingAnalyse alternative splicing (including intron retention(s))
analyzeCPATImport Result of External Sequence Analysis
analyzeCPC2Import Result of External Sequence Analysis
analyzeIUPred2AImport Result of IUPred2A analysis
analyzeNetSurf2Import Result of NetSurfP2 analysis
analyzeNovelIsoformORFPrediction of Isoform Open Reading Frames.
analyzeORFPrediction 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
extractGeneExpressionExtract raw gene counts or abundances from a...
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...
extractSplicingSummaryExtracts 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
importSalmonDataDirect creation of a switchAnalyzeRlist from Salmon...
isoformSwitchAnalysisCombinedIsoform Switch Analysis Workflow: Extract, Annotate 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...
isoformToGeneExpSum transcript/isoform expression to gene get level...
isoformToIsoformFractionCalculate isoform fraction from isoform abundance matrix
preFilterFiltering of a switchAnalyzeRlist
prepareSalmonFilesDataFramePrepare data.frame needed run importSalmonData.
subsetSwitchAnalyzeRlistA function which subset all entries in a switchAnalyzeRlist.
switchAnalyzeRlistCreate a switchAnalyzeRlist Object
switchPlotIsoform Switch Analysis Plot
switchPlotTopSwitchesCreating the Isoform Switch Analysis Plot for the Top...
switchPlotTranscriptPlot Transcript Structure and Annotation
testDataExample data for IsoformSwitchAnalyzeR
kvittingseerup/IsoformSwitchAnalyzeR documentation built on May 12, 2021, 12:25 p.m.