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
