Files in ste-depo/INSPEcT
Modeling RNA synthesis, processing and degradation with RNA-seq data
DESCRIPTION
NAMESPACE
R/AllClasses.R
R/AllGenerics.R
R/AllInternalFunctions.R
R/Extract-methods.R
R/INSPEcT-GUI-functions.R
R/INSPEcT-GUI-server.R
R/INSPEcT-GUI-ui.R
R/ProcessingRateDelay-server.R
R/ProcessingRateDelay-ui.R
R/ProcessingRateDelayAPP-functions.R
R/chisqtest-methods.R
R/computeConfidenceIntervals.R
R/correlationPlot-methods.R
R/dataDocumentation.R
R/geneClass-methods.R
R/inHeatmap-methods.R
R/logLik-methods.R
R/makeModelRates-methods.R
R/makeOscillatorySimModel-methods.R
R/makeSimDataset-methods.R
R/makeSimModel-methods.R
R/modelRates-methods.R
R/modelRatesNF-methods.R
R/modelSelection-methods.R
R/modelingParams-methods.R
R/newINSPEcT-functions.R
R/plotGene-methods.R
R/processingRateDelay-methods.R
R/quantifyExpressionsFromBAMs.R
R/quantifyExpressionsFromBWs.R
R/quantifyExpressionsFromTrAbundance.R
R/quantifyExpressionsFromTrCounts-functions.R
R/ratePvals-methods.R
R/ratesFirstGuess-methods.R
R/rocCurve-methods.R
R/rocThresholds-methods.R
R/runShinyApps.R
R/setConfidenceIntervals-method.R
R/show-methods.R
R/steady-state-methods.R
R/steadyNoNascent-methods.R
R/viewConfidenceIntervals-methods.R
R/viewModelRates-methods.R
R/wrap-up-functions.R
data/allcounts.RData
data/datalist
data/featureWidths.RData
data/libsizes.RData
data/matureSim2replicates.RData
data/matureSim3replicates.RData
data/nascentSim2replicates.RData
data/nascentSim3replicates.RData
inst/CITATION
inst/INSPEcT_GUI_sample_dataset.rds
inst/NEWS
inst/extdata/bamRep1.bam
inst/extdata/bamRep2.bam
inst/extdata/bamRep3.bam
inst/extdata/bamRep4.bam
inst/nascentAnnTabPCR.csv
inst/nascentInspObj.rds
inst/nascentInspObj10.rds
inst/totalAnnTabPCR.csv
man/AIC-INSPEcT-method.Rd
man/Extract.Rd
man/INSPEcT-class.Rd
man/INSPEcT-shinyApps.Rd
man/INSPEcT.Rd
man/INSPEcT_diffsteady-class.Rd
man/INSPEcT_model-class.Rd
man/INSPEcT_steadyNoNascent-class.Rd
man/PTratio.Rd
man/PTreg.Rd
man/allcounts.Rd
man/calculateRatePvals.Rd
man/chisqmodel.Rd
man/chisqtest.Rd
man/combine.Rd
man/compareSteady.Rd
man/compareSteadyNoNascent.Rd
man/computeConfidenceIntervals.Rd
man/convergence.Rd
man/correlationPlot.Rd
man/dim-INSPEcT-method.Rd
man/featureNames-INSPEcT-method.Rd
man/featureWidths.Rd
man/geneClass.Rd
man/inHeatmap.Rd
man/inspectFromBAM.Rd
man/inspectFromPCR.Rd
man/labeledSF.Rd
man/libsizes.Rd
man/logLik.Rd
man/makeModelRates.Rd
man/makeOscillatorySimModel.Rd
man/makeSimDataset.Rd
man/makeSimModel.Rd
man/mature.Rd
man/matureVar.Rd
man/modelRates.Rd
man/modelRatesNF.Rd
man/modelSelection.Rd
man/modelingParams.Rd
man/nGenes.Rd
man/nTpts.Rd
man/newINSPEcT.Rd
man/plotGene.Rd
man/plotMA.Rd
man/plotPMgene.Rd
man/plotPMtrend.Rd
man/premature.Rd
man/prematureVar.Rd
man/processingDelay.Rd
man/quantifyExpressionsFromBAMs.Rd
man/quantifyExpressionsFromBWs.Rd
man/quantifyExpressionsFromTrAbundance.Rd
man/quantifyExpressionsFromTrCounts.Rd
man/ratePvals.Rd
man/ratesFirstGuess.Rd
man/ratesFirstGuessVar.Rd
man/removeModel.Rd
man/rocCurve.Rd
man/rocThresholds.Rd
man/setConfidenceIntervals.Rd
man/simData3rep_Nascent.Rd
man/simData3rep_NoNascent.Rd
man/simData4rep_Nascent.Rd
man/simData4rep_NoNascent.Rd
man/split.Rd
man/tpts.Rd
man/viewConfidenceIntervals.Rd
man/viewModelRates.Rd
vignettes/INSPEcT.Rmd
vignettes/INSPEcT_GUI.rmd
vignettes/INSPEcT_GUI_figures/INSPEcT_GUI.png
vignettes/INSPEcT_GUI_figures/case_study_1.png
vignettes/INSPEcT_GUI_figures/case_study_2.png
vignettes/INSPEcT_GUI_figures/case_study_3.png
vignettes/INSPEcT_GUI_figures/case_study_4.png
vignettes/INSPEcT_GUI_figures/minimization_status.png
vignettes/INSPEcT_GUI_figures/rates_and_concentrations_panel.png
vignettes/INSPEcT_GUI_figures/rates_functional_forms.png
vignettes/INSPEcT_GUI_figures/select_INSPEcT_object_class_gene.png
vignettes/bibliography.bib
