Files in INSPEcT
Modeling RNA synthesis, processing and degradation with RNA-seq data

NAMESPACE
DESCRIPTION
build/vignette.rds
data/allcounts.RData
data/nascentSim2replicates.RData
data/featureWidths.RData
data/datalist
data/libsizes.RData
data/matureSim3replicates.RData
data/matureSim2replicates.RData
data/nascentSim3replicates.RData
R/modelingParams-methods.R R/ratesFirstGuess-methods.R R/dataDocumentation.R R/INSPEcT-GUI-functions.R R/inHeatmap-methods.R R/geneClass-methods.R R/quantifyExpressionsFromBWs.R R/modelRates-methods.R R/show-methods.R R/ratePvals-methods.R R/ProcessingRateDelay-ui.R R/quantifyExpressionsFromTrAbundance.R R/AllGenerics.R R/wrap-up-functions.R R/setConfidenceIntervals-method.R R/plotGene-methods.R R/steady-state-methods.R R/modelSelection-methods.R R/runShinyApps.R R/ProcessingRateDelayAPP-functions.R R/modelRatesNF-methods.R R/INSPEcT-GUI-ui.R R/correlationPlot-methods.R R/rocCurve-methods.R R/computeConfidenceIntervals.R R/makeModelRates-methods.R R/compareSteadyNoNascent-methods.R R/steadyNoNascent-methods.R R/logLik-methods.R R/viewConfidenceIntervals-methods.R R/makeSimDataset-methods.R R/viewModelRates-methods.R R/AllInternalFunctions.R R/quantifyExpressionsFromTrCounts-functions.R R/Extract-methods.R R/AllClasses.R R/quantifyExpressionsFromBAMs.R R/rocThresholds-methods.R R/makeSimModel-methods.R R/makeOscillatorySimModel-methods.R R/chisqtest-methods.R R/newINSPEcT-functions.R R/processingRateDelay-methods.R R/INSPEcT-GUI-server.R R/ProcessingRateDelay-server.R vignettes/INSPEcT_GUI.rmd
vignettes/bibliography.bib
vignettes/INSPEcT.Rmd
vignettes/INSPEcT_GUI_figures/case_study_2.png
vignettes/INSPEcT_GUI_figures/rates_functional_forms.png
vignettes/INSPEcT_GUI_figures/minimization_status.png
vignettes/INSPEcT_GUI_figures/case_study_3.png
vignettes/INSPEcT_GUI_figures/select_INSPEcT_object_class_gene.png
vignettes/INSPEcT_GUI_figures/rates_and_concentrations_panel.png
vignettes/INSPEcT_GUI_figures/INSPEcT_GUI.png
vignettes/INSPEcT_GUI_figures/case_study_4.png
vignettes/INSPEcT_GUI_figures/case_study_1.png
man/makeSimDataset.Rd man/allcounts.Rd man/PTreg.Rd man/PTratio.Rd man/plotGene.Rd man/makeOscillatorySimModel.Rd man/matureVar.Rd man/inspectFromBAM.Rd man/simData4rep_Nascent.Rd man/ratePvals.Rd man/viewConfidenceIntervals.Rd man/correlationPlot.Rd man/removeModel.Rd man/quantifyExpressionsFromBAMs.Rd man/rocThresholds.Rd man/makeSimModel.Rd man/plotPMtrend.Rd man/chisqtest.Rd man/quantifyExpressionsFromBWs.Rd man/viewModelRates.Rd man/modelingParams.Rd man/featureNames-INSPEcT-method.Rd man/Extract.Rd man/prematureVar.Rd man/plotPMgene.Rd man/computeConfidenceIntervals.Rd man/ratesFirstGuess.Rd man/makeModelRates.Rd man/INSPEcT_steadyNoNascent-class.Rd man/INSPEcT-class.Rd man/modelRatesNF.Rd man/inspectFromPCR.Rd man/combine.Rd man/labeledSF.Rd man/compareSteady.Rd man/convergence.Rd man/mature.Rd man/modelRates.Rd man/AIC-INSPEcT-method.Rd man/logLik.Rd man/dim-INSPEcT-method.Rd man/geneClass.Rd man/featureWidths.Rd man/libsizes.Rd man/tpts.Rd man/nGenes.Rd man/simData4rep_NoNascent.Rd man/modelSelection.Rd man/simData3rep_Nascent.Rd man/quantifyExpressionsFromTrAbundance.Rd man/processingDelay.Rd man/ratesFirstGuessVar.Rd man/nTpts.Rd man/simData3rep_NoNascent.Rd man/INSPEcT.Rd man/inHeatmap.Rd man/INSPEcT-shinyApps.Rd man/premature.Rd man/compareSteadyNoNascent.Rd man/chisqmodel.Rd man/setConfidenceIntervals.Rd man/quantifyExpressionsFromTrCounts.Rd man/calculateRatePvals.Rd man/rocCurve.Rd man/split.Rd man/plotMA.Rd man/INSPEcT_model-class.Rd man/newINSPEcT.Rd man/INSPEcT_diffsteady-class.Rd
inst/nascentAnnTabPCR.csv
inst/INSPEcT_GUI_sample_dataset.rds
inst/totalAnnTabPCR.csv
inst/nascentInspObj.rds
inst/NEWS
inst/CITATION
inst/nascentInspObj10.rds
inst/doc/INSPEcT_GUI.rmd inst/doc/INSPEcT_GUI.R
inst/doc/INSPEcT.html
inst/doc/INSPEcT.R inst/doc/INSPEcT.Rmd
inst/doc/INSPEcT_GUI.html
inst/extdata/bamRep4.bam
inst/extdata/bamRep1.bam
inst/extdata/bamRep2.bam
inst/extdata/bamRep3.bam
INSPEcT documentation built on April 29, 2020, 5:19 a.m.