Man pages for kvittingseerup/IsoformSwitchAnalyzeR
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data
| addORFfromGTF | Add CDS from a GTF file to a switchAnalyzeRlist. |
| analyzeAlternativSplicing | 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 |
| analyzeIUPred2A | Import Result of IUPred2A or IUPred3 analysis |
| analyzeNetSurfP3 | Import Result of NetSurfP3 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 |
| expressionAnalysisPlots | Plots for Analyzing Expression and Isoform Usage |
| extractConsequenceEnrichment | Analyze data for enrichment of specific consequences |
| extractConsequenceEnrichmentComparison | Compare enrichment of specific consequences between... |
| extractConsequenceSummary | Analyze Switch Consequences |
| extractGeneExpression | Extract raw gene counts or abundances from a... |
| extractGenomeWideAnalysis | Genome wide Analysis of Consequences due to isoform switching |
| extractGenomeWideSplicingAnalysis | Genome wide Analysis of alternative splicing |
| extractSequence | Extract nucloetide (and amino acid) sequence of transcripts. |
| extractSplicingEnrichment | Analyze data for enrichment of specific type of alternative... |
| extractSplicingEnrichmentComparison | Compare enrichment of specific type 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. |
| importCufflinksGalaxyData | Import CuffDiff (Cufflinks) Data Into R |
| importGTF | Import Transcripts from a GTF file into R |
| importIsoformExpression | Import expression data from Kallisto, Salmon, RSEM or... |
| importRdata | Create SwitchAnalyzeRlist From Standard R Objects |
| importSalmonData | Direct creation of a switchAnalyzeRlist from Salmon... |
| isoformSwitchAnalysisCombined | Isoform Switch Analysis Workflow: Extract, Annotate and... |
| isoformSwitchAnalysisPart1 | Isoform Switch Analysis Workflow Part 1: Extract Isoform... |
| isoformSwitchAnalysisPart2 | Isoform Switch Analysis Workflow Part 2: Plot All Isoform... |
| IsoformSwitchTestDEXSeq | Statistical Test for identifying Isoform Switching via DEXSeq |
| IsoformSwitchTestSatuRn | Statistical Test for identifying Isoform Switching via... |
| isoformToGeneExp | Sum transcript/isoform expression to gene get level... |
| isoformToIsoformFraction | Calculate isoform fraction from isoform abundance matrix |
| preFilter | Filtering of a switchAnalyzeRlist |
| prepareSalmonFilesDataFrame | Prepare data.frame needed run importSalmonData. |
| subsetSwitchAnalyzeRlist | A function which subset all entries in a switchAnalyzeRlist. |
| switchAnalyzeRlist | Create a switchAnalyzeRlist Object |
| switchPlot | Isoform Switch Analysis Plot |
| switchPlotTopSwitches | Creating the Isoform Switch Analysis Plot for the Top... |
| switchPlotTranscript | Plot Transcript Structure and Annotation |
| testData | Example data for IsoformSwitchAnalyzeR |
