Files in kvittingseerup/IsoformSwitchAnalyzeR
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

.DS_Store
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/analyze_ORF.R R/analyze_alternative_splicing.R R/analyze_external_sequence_analysis.R R/analyze_switch_consequences.R R/classes.R R/high_level_functions.R R/import_data.R R/isoform_plots.R R/methods.R R/plot_all_iso_switch.R R/test_isoform_switches.R R/tools.R README.md
data/exampleSwitchList.RData
data/exampleSwitchListAnalyzed.RData
data/exampleSwitchListIntermediary.RData
inst/.DS_Store
inst/CITATION
inst/NEWS
inst/extdata/DeepTMHMM.gff3
inst/extdata/Fibroblasts_0/quant.sf.gz
inst/extdata/Fibroblasts_1/quant.sf.gz
inst/extdata/cpat_results.txt
inst/extdata/cpc2_result.txt
inst/extdata/deeploc2.csv
inst/extdata/drosophila/data_cond1_rep1/aux_info/meta_info.json
inst/extdata/drosophila/data_cond1_rep1/cmd_info.json
inst/extdata/drosophila/data_cond1_rep1/quant.sf.gz
inst/extdata/drosophila/data_cond1_rep2/aux_info/meta_info.json
inst/extdata/drosophila/data_cond1_rep2/cmd_info.json
inst/extdata/drosophila/data_cond1_rep2/quant.sf.gz
inst/extdata/drosophila/data_cond2_rep1/aux_info/meta_info.json
inst/extdata/drosophila/data_cond2_rep1/cmd_info.json
inst/extdata/drosophila/data_cond2_rep1/quant.sf.gz
inst/extdata/drosophila/data_cond2_rep2/aux_info/meta_info.json
inst/extdata/drosophila/data_cond2_rep2/cmd_info.json
inst/extdata/drosophila/data_cond2_rep2/quant.sf.gz
inst/extdata/example.gtf.gz
inst/extdata/example_isoform_nt.fasta.gz
inst/extdata/hESC_0/quant.sf.gz
inst/extdata/hESC_1/quant.sf.gz
inst/extdata/iPS_0/quant.sf.gz
inst/extdata/iPS_1/quant.sf.gz
inst/extdata/iupred2a_result.txt.gz
inst/extdata/netsurfp3_result.csv.gz
inst/extdata/pfam_results.txt
inst/extdata/signalP_results.txt
man/.Rapp.history
man/IsoformSwitchTestDEXSeq.Rd man/IsoformSwitchTestSatuRn.Rd man/addORFfromGTF.Rd man/analyzeAlternativSplicing.Rd man/analyzeCPAT.Rd man/analyzeCPC2.Rd man/analyzeDeepLoc2.Rd man/analyzeDeepTMHMM.Rd man/analyzeIUPred2A.Rd man/analyzeNetSurfP3.Rd man/analyzeNovelIsoformORF.Rd man/analyzeORF.Rd man/analyzePFAM.Rd man/analyzeSignalP.Rd man/analyzeSwitchConsequences.Rd man/expressionAnalysisPlots.Rd man/extractConsequenceEnrichment.Rd man/extractConsequenceEnrichmentComparison.Rd man/extractConsequenceSummary.Rd man/extractGeneExpression.Rd man/extractGenomeWideAnalysis.Rd man/extractGenomeWideSplicingAnalysis.Rd man/extractSequence.Rd man/extractSplicingEnrichment.Rd man/extractSplicingEnrichmentComparison.Rd man/extractSplicingSummary.Rd man/extractSubCellShifts.Rd man/extractSwitchOverlap.Rd man/extractSwitchSummary.Rd man/extractTopSwitches.Rd man/importCufflinksGalaxyData.Rd man/importGTF.Rd man/importIsoformExpression.Rd man/importRdata.Rd man/importSalmonData.Rd man/isoformSwitchAnalysisCombined.Rd man/isoformSwitchAnalysisPart1.Rd man/isoformSwitchAnalysisPart2.Rd man/isoformToGeneExp.Rd man/isoformToIsoformFraction.Rd man/preFilter.Rd man/prepareSalmonFilesDataFrame.Rd man/subsetSwitchAnalyzeRlist.Rd man/switchAnalyzeRlist.Rd man/switchPlot.Rd man/switchPlotTopSwitches.Rd man/switchPlotTranscript.Rd man/testData.Rd
src/utils.c
vignettes/IsoformSwitchAnalyzeR.Rmd
vignettes/Overview_figure_detailed.jpg
vignettes/Overview_figure_simple.jpg
kvittingseerup/IsoformSwitchAnalyzeR documentation built on June 28, 2024, 5:41 p.m.