├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── R ├── analyze_ORF.R ├── analyze_alternative_splicing.R ├── analyze_external_sequence_analysis.R ├── analyze_switch_consequences.R ├── classes.R ├── high_level_functions.R ├── import_data.R ├── isoform_plots.R ├── methods.R ├── plot_all_iso_switch.R ├── test_isoform_switches.R └── tools.R ├── README.md ├── data ├── exampleSwitchList.RData ├── exampleSwitchListAnalyzed.RData └── exampleSwitchListIntermediary.RData ├── inst ├── CITATION ├── NEWS └── extdata │ ├── DeepTMHMM.gff3 │ ├── Fibroblasts_0 │ └── quant.sf.gz │ ├── Fibroblasts_1 │ └── quant.sf.gz │ ├── cpat_results.txt │ ├── cpc2_result.txt │ ├── deeploc2.csv │ ├── drosophila │ ├── data_cond1_rep1 │ │ ├── aux_info │ │ │ └── meta_info.json │ │ ├── cmd_info.json │ │ └── quant.sf.gz │ ├── data_cond1_rep2 │ │ ├── aux_info │ │ │ └── meta_info.json │ │ ├── cmd_info.json │ │ └── quant.sf.gz │ ├── data_cond2_rep1 │ │ ├── aux_info │ │ │ └── meta_info.json │ │ ├── cmd_info.json │ │ └── quant.sf.gz │ └── data_cond2_rep2 │ │ ├── aux_info │ │ └── meta_info.json │ │ ├── cmd_info.json │ │ └── quant.sf.gz │ ├── example.gtf.gz │ ├── example_isoform_nt.fasta.gz │ ├── hESC_0 │ └── quant.sf.gz │ ├── hESC_1 │ └── quant.sf.gz │ ├── iPS_0 │ └── quant.sf.gz │ ├── iPS_1 │ └── quant.sf.gz │ ├── iupred2a_result.txt.gz │ ├── netsurfp3_result.csv.gz │ ├── pfam_results.txt │ └── signalP_results.txt ├── man ├── .Rapp.history ├── IsoformSwitchTestDEXSeq.Rd ├── IsoformSwitchTestSatuRn.Rd ├── addORFfromGTF.Rd ├── analyzeAlternativSplicing.Rd ├── analyzeCPAT.Rd ├── analyzeCPC2.Rd ├── analyzeDeepLoc2.Rd ├── analyzeDeepTMHMM.Rd ├── analyzeIUPred2A.Rd ├── analyzeNetSurfP3.Rd ├── analyzeNovelIsoformORF.Rd ├── analyzeORF.Rd ├── analyzePFAM.Rd ├── analyzeSignalP.Rd ├── analyzeSwitchConsequences.Rd ├── exportToPairedGSEA.Rd ├── expressionAnalysisPlots.Rd ├── extractConsequenceEnrichment.Rd ├── extractConsequenceEnrichmentComparison.Rd ├── extractConsequenceSummary.Rd ├── extractGeneExpression.Rd ├── extractGenomeWideAnalysis.Rd ├── extractGenomeWideSplicingAnalysis.Rd ├── extractSequence.Rd ├── extractSplicingEnrichment.Rd ├── extractSplicingEnrichmentComparison.Rd ├── extractSplicingSummary.Rd ├── extractSubCellShifts.Rd ├── extractSwitchOverlap.Rd ├── extractSwitchSummary.Rd ├── extractTopSwitches.Rd ├── importCufflinksGalaxyData.Rd ├── importGTF.Rd ├── importIsoformExpression.Rd ├── importPairedGSEA.Rd ├── importRdata.Rd ├── importSalmonData.Rd ├── isoformSwitchAnalysisCombined.Rd ├── isoformSwitchAnalysisPart1.Rd ├── isoformSwitchAnalysisPart2.Rd ├── isoformToGeneExp.Rd ├── isoformToIsoformFraction.Rd ├── preFilter.Rd ├── prepareSalmonFilesDataFrame.Rd ├── subsetSwitchAnalyzeRlist.Rd ├── switchAnalyzeRlist.Rd ├── switchPlot.Rd ├── switchPlotTopSwitches.Rd ├── switchPlotTranscript.Rd └── testData.Rd ├── src └── utils.c └── vignettes ├── IsoformSwitchAnalyzeR.Rmd ├── Overview_figure_detailed.jpg └── Overview_figure_simple.jpg /.Rbuildignore: 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