Files in IsoformSwitchAnalyzeR

Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.

README.md

NAMESPACE

DESCRIPTION

build/vignette.rds

src/utils.c

data/exampleSwitchListAnalyzed.RData

data/exampleSwitchList.RData

data/exampleSwitchListIntermediary.RData

R/analyze_ORF.R R/high_level_functions.R R/tools.R R/test_isoform_switches.R R/classes.R R/analyze_switch_consequences.R R/import_data.R R/analyze_alternative_splicing.R R/isoform_plots.R R/methods.R R/analyze_external_sequence_analysis.R R/plot_all_iso_switch.R

vignettes/Overview_figure_simple.jpg

vignettes/IsoformSwitchAnalyzeR.Rmd

vignettes/Overview_figure_detailed.jpg

man/switchAnalyzeRlist.Rd man/importIsoformExpression.Rd man/IsoformSwitchTestDRIMSeq.Rd man/importCufflinksGalaxyData.Rd man/extractSwitchSummary.Rd man/isoformToIsoformFraction.Rd man/extractSplicingEnrichmentComparison.Rd man/subsetSwitchAnalyzeRlist.Rd man/extractConsequenceEnrichment.Rd man/extractGeneExpression.Rd man/expressionAnalysisPlots.Rd man/importSalmonData.Rd man/isoformSwitchAnalysisPart1.Rd man/extractGenomeWideAnalysis.Rd man/analyzeSignalP.Rd man/analyzePFAM.Rd man/extractGenomeWideSplicingAnalysis.Rd man/analyzeNetSurf2.Rd man/extractSwitchOverlap.Rd man/extractSplicingEnrichment.Rd man/testData.Rd man/isoformSwitchAnalysisCombined.Rd man/importGTF.Rd man/extractTopSwitches.Rd man/CDSSet.Rd man/preFilter.Rd man/importRdata.Rd man/extractConsequenceSummary.Rd man/analyzeIUPred2A.Rd man/analyzeCPC2.Rd man/analyzeAlternativSplicing.Rd man/extractSplicingSummary.Rd man/extractConsequenceEnrichmentComparison.Rd man/analyzeCPAT.Rd man/isoformToGeneExp.Rd man/IsoformSwitchTestDEXSeq.Rd man/getCDS.Rd man/analyzeSwitchConsequences.Rd man/switchPlot.Rd man/prepareSalmonFilesDataFrame.Rd man/isoformSwitchAnalysisPart2.Rd man/switchPlotTopSwitches.Rd man/extractSequence.Rd man/switchPlotTranscript.Rd man/analyzeORF.Rd

inst/NEWS

inst/CITATION

inst/doc/IsoformSwitchAnalyzeR.R inst/doc/IsoformSwitchAnalyzeR.Rmd

inst/doc/IsoformSwitchAnalyzeR.html

inst/extdata/signalP_results.txt

inst/extdata/pfam_results.txt

inst/extdata/cpat_results.txt

inst/extdata/cpc2_result.txt

inst/extdata/example_isoform_nt.fasta.gz

inst/extdata/iupred2a_result.txt.gz

inst/extdata/example.gtf.gz

inst/extdata/hESC_1/quant.sf.gz

inst/extdata/iPS_1/quant.sf.gz

inst/extdata/Fibroblasts_1/quant.sf.gz

inst/extdata/Fibroblasts_0/quant.sf.gz

inst/extdata/hESC_0/quant.sf.gz

inst/extdata/drosophila/data_cond2_rep1/quant.sf.gz

inst/extdata/drosophila/data_cond2_rep1/cmd_info.json

inst/extdata/drosophila/data_cond2_rep1/aux_info/meta_info.json

inst/extdata/drosophila/data_cond1_rep1/quant.sf.gz

inst/extdata/drosophila/data_cond1_rep1/cmd_info.json

inst/extdata/drosophila/data_cond1_rep1/aux_info/meta_info.json

inst/extdata/drosophila/data_cond2_rep2/quant.sf.gz

inst/extdata/drosophila/data_cond2_rep2/cmd_info.json

inst/extdata/drosophila/data_cond2_rep2/aux_info/meta_info.json

inst/extdata/drosophila/data_cond1_rep2/quant.sf.gz

inst/extdata/drosophila/data_cond1_rep2/cmd_info.json

inst/extdata/drosophila/data_cond1_rep2/aux_info/meta_info.json

inst/extdata/iPS_0/quant.sf.gz

IsoformSwitchAnalyzeR documentation built on Nov. 8, 2020, 5:36 p.m.