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"dim-INSPEcT-method", "title": "Dimensions of an Object of Class INSPEcT", "topics": [ "dim,INSPEcT-method" ] }, { "page": "Extract", "title": "Extract Parts of an INSPEcT or an INSPEcT_model Object", "topics": [ "Extract", "[,INSPEcT,ANY,ANY,ANY-method", "[,INSPEcT_diffsteady,ANY,ANY,ANY-method", "[,INSPEcT_model,ANY,ANY,ANY-method" ] }, { "page": "featureNames-INSPEcT-method", "title": "Gene Names Associated with an Object of Class INSPEcT", "topics": [ "featureNames,INSPEcT-method", "featureNames<-,INSPEcT-method" ] }, { "page": "featureWidths", "title": "Contains two variables: \"exWdths\" and \"intWdths\" containing the lenght of the exons and introns, respectively, relative to the genes in \"allcounts\"", "topics": [ "featureWidths" ] }, { "page": "geneClass", "title": "Retrieve the regulatory class for each gene", "topics": [ "geneClass", "geneClass,INSPEcT-method", "geneClass,INSPEcT_diffsteady-method", "geneClass,INSPEcT_model-method" ] }, { "page": "inHeatmap", "title": "Heatmap that represent the fold changes of all the five features", "topics": [ "inHeatmap", "inHeatmap,INSPEcT-method" ] }, { "page": "INSPEcT", "title": "INSPEcT package", "topics": [ "INSPEcT" ] }, { "page": "INSPEcT_diffsteady-class", "title": "An S4 class to represent comparisons between two steady-state conditions", "topics": [ "degradation", "degradation,INSPEcT_diffsteady-method", "featureNames,INSPEcT_diffsteady-method", "INSPEcT_diffsteady-class", "processing", "processing,INSPEcT_diffsteady-method", "show,INSPEcT_diffsteady-method", "synthesis", "synthesis,INSPEcT_diffsteady-method" ] }, { "page": "INSPEcT_model-class", "title": "An S4 class to represent models generated by INSPEcT", "topics": [ "INSPEcT_model-class", "show,INSPEcT_model-method" ] }, { "page": "INSPEcT_steadyNoNascent-class", "title": "An S4 class to represent steady-state analysis without nascent RNA", "topics": [ "INSPEcT_steadyNoNascent-class", "show,INSPEcT_steadyNoNascent-method", "[,INSPEcT_steadyNoNascent,ANY,ANY,ANY-method" ] }, { "page": "INSPEcT-class", "title": "An S4 class to contain all rates and models generated by INSPEcT", "topics": [ "INSPEcT-class", "show,INSPEcT-method" ] }, { "page": "INSPEcT-shinyApps", "title": "Run shiny applications contained in the package INSPEcT", "topics": [ "INSPEcT-shinyApps", "runINSPEcTGUI", "runProcessingRateDelay" ] }, { "page": "inspectFromBAM", "title": "Wrapper function from BAM files", "topics": [ "inspectFromBAM" ] }, { "page": "inspectFromPCR", "title": "Wrapper function from PCR quantifications", "topics": [ "inspectFromPCR" ] }, { "page": "labeledSF", "title": "Accessor to the slot labeledSF of an INSPEcT object", "topics": [ "labeledSF", "labeledSF,INSPEcT-method" ] }, { "page": "libsizes", "title": "Contains two variables: \"nascentLS\" and \"totalLS\" containing the sequencing depth of nascent and total libraries respectively, relative to the experiments in \"allcounts\"", "topics": [ "libsizes" ] }, { "page": "logLik", "title": "Retrieve results of log likelihood test", "topics": [ "logLik", "logLik,INSPEcT-method", "logLik,INSPEcT_model-method" ] }, { "page": "makeModelRates", "title": "Calculate modeled rates and concentrations", "topics": [ "makeModelRates", "makeModelRates,INSPEcT-method", "makeModelRates,INSPEcT_model-method" ] }, { "page": "makeOscillatorySimModel", "title": "Build the synthetic rates with oscillatory pattern", "topics": [ "makeOscillatorySimModel", "makeOscillatorySimModel,INSPEcT-method" ] }, { "page": "makeSimDataset", "title": "Generate synthetic rates and concentrations", "topics": [ "makeSimDataset", "makeSimDataset,INSPEcT_model-method" ] }, { "page": "makeSimModel", "title": "Build the synthetic rates shaped on a dataset", "topics": [ "makeSimModel", "makeSimModel,INSPEcT-method" ] }, { "page": "mature", "title": "Get mature RNA expressions from an object of class INSPEcT_diffsteady", "topics": [ "mature", "mature,INSPEcT_steadyNoNascent-method" ] }, { "page": "matureVar", "title": "Get mature RNA expressions variances from an object of class INSPEcT_diffsteady", "topics": [ "matureVar", "matureVar,INSPEcT_steadyNoNascent-method" ] }, { "page": "modelingParams", "title": "Get and set number parameters for the modeling", "topics": [ "modelingParams", "modelingParams,INSPEcT-method" ] }, { "page": "modelRates", "title": "Launch the modeling process", "topics": [ "modelRates", "modelRates,INSPEcT-method" ] }, { "page": "modelRatesNF", "title": "Launch the modeling process without imposing sigmoid/impulse functional form", "topics": [ "modelRatesNF", "modelRatesNF,INSPEcT-method" ] }, { "page": "modelSelection", "title": "Visualize criteria used for rate variability", "topics": [ "modelSelection", "modelSelection,INSPEcT-method", "modelSelection,INSPEcT_model-method" ] }, { "page": "newINSPEcT", "title": "Create a new INSPEcT object", "topics": [ "newINSPEcT" ] }, { "page": "nGenes", "title": "Get the number of genes within the INSPEcT object", "topics": [ "nGenes", "nGenes,INSPEcT-method" ] }, { "page": "nTpts", "title": "Get the number of time points within the INSPEcT object", "topics": [ "nTpts", "nTpts,INSPEcT-method" ] }, { "page": "plotGene", "title": "Plot the pre-modeled and modeled profiles for one gene", "topics": [ "plotGene", "plotGene,INSPEcT-method" ] }, { "page": "plotMA", "title": "MA-plot from base means and log fold changes", "topics": [ "plotMA", "plotMA,INSPEcT_diffsteady-method" ] }, { "page": "plotPMgene", "title": "Plot the premature/mature expression of a gene and the global trend from an object of class INSPEcT_diffsteady", "topics": [ "plotPMgene", "plotPMgene,INSPEcT_steadyNoNascent-method" ] }, { "page": "plotPMtrend", "title": "Plot the premature/mature trend from an object of class INSPEcT_diffsteady", "topics": [ "plotPMtrend", "plotPMtrend,INSPEcT_steadyNoNascent-method" ] }, { "page": "premature", "title": "Get premature RNA expressions from an object of class INSPEcT_diffsteady", "topics": [ "premature", "premature,INSPEcT_steadyNoNascent-method" ] }, { "page": "prematureVar", "title": "Get premature RNA expressions variances from an object of class INSPEcT_diffsteady", "topics": [ "prematureVar", "prematureVar,INSPEcT_steadyNoNascent-method" ] }, { "page": "processingDelay", "title": "Classify genes as delayed by the processing using the delta and tau metrics", "topics": [ "calculateDelta", "calculateDelta,INSPEcT-method", "calculateTau", "calculateTau,INSPEcT-method", "processingDelay", "processingDelay,INSPEcT-method" ] }, { "page": "PTratio", "title": "Calculate post-transcriptional ratio from an object of class INSPEcT_diffsteady", "topics": [ "PTratio", "PTratio,INSPEcT_steadyNoNascent-method" ] }, { "page": "PTreg", "title": "Calculate the post-transcriptional ratio from an object of class INSPEcT_diffsteady", "topics": [ "PTreg", "PTreg,INSPEcT_steadyNoNascent-method" ] }, { "page": "quantifyExpressionsFromBAMs", "title": "Evaluate introns and exons expressions from BAM or SAM files", "topics": [ "quantifyExpressionsFromBAMs" ] }, { "page": "quantifyExpressionsFromBWs", "title": "Evaluate introns and exons expressions from BAM or SAM files", "topics": [ "quantifyExpressionsFromBWs" ] }, { "page": "quantifyExpressionsFromTrAbundance", "title": "Given introns and exons abundances (for example RPKMs) this method returns their variances evaluated thorugh plgem.", "topics": [ "quantifyExpressionsFromTrAbundance" ] }, { "page": "quantifyExpressionsFromTrCounts", "title": "Evaluates introns and exons RPKMs, per gene, from counts data.", "topics": [ "quantifyExpressionsFromTrCounts" ] }, { "page": "ratePvals", "title": "Retrieve a single p-value for each rate", "topics": [ "ratePvals", "ratePvals,INSPEcT-method" ] }, { "page": "ratesFirstGuess", "title": "Retrieve pre-modeling rates and concentrations", "topics": [ "ratesFirstGuess", "ratesFirstGuess,INSPEcT-method" ] }, { "page": "ratesFirstGuessVar", "title": "Retrieve pre-modeling rates and concentrations variance", "topics": [ "ratesFirstGuessVar", "ratesFirstGuessVar,INSPEcT-method" ] }, { "page": "removeModel", "title": "remove modelling information from INSPEcT object", "topics": [ "removeModel", "removeModel,INSPEcT-method" ] }, { "page": "rocCurve", "title": "Display rate classification performance", "topics": [ "rocCurve", "rocCurve,INSPEcT_model,INSPEcT-method" ] }, { "page": "rocThresholds", "title": "Display rate classification performance with thresholds visible at x-axis", "topics": [ "rocThresholds", "rocThresholds,INSPEcT_model,INSPEcT-method" ] }, { "page": "setConfidenceIntervals", "title": "Set confidence intervals", "topics": [ "setConfidenceIntervals", "setConfidenceIntervals,INSPEcT-method" ] }, { "page": "simData3rep_Nascent", "title": "An INSPEcT object with 1000 simulated rates and concentration and their modeled rates", "topics": [ "simData3rep_Nascent" ] }, { "page": "simData3rep_NoNascent", "title": "An INSPEcT object with 1000 simulated rates and concentration and their modeled rates", "topics": [ "simData3rep_NoNascent" ] }, { "page": "simData4rep_Nascent", "title": "An INSPEcT object with 1000 simulated rates and concentration and their modeled rates", "topics": [ "simData4rep_Nascent" ] }, { "page": "simData4rep_NoNascent", "title": "An INSPEcT object with 1000 simulated rates and concentration and their modeled rates", "topics": [ "simData4rep_NoNascent" ] }, { "page": "split", "title": "Divide an INSPEcT Object into groups", "topics": [ "split", "split,INSPEcT,ANY-method" ] }, { "page": "tpts", "title": "Accessor to the slot tpts of an INSPEcT object", "topics": [ "tpts", "tpts,INSPEcT-method" ] }, { "page": "viewConfidenceIntervals", "title": "Retrieve the modeled Confidence Intervals", "topics": [ "viewConfidenceIntervals", "viewConfidenceIntervals,INSPEcT-method" ] }, { "page": "viewModelRates", "title": "Retrieve the modeled rates and concentrations", "topics": [ "viewModelRates", 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intervals estimation and selection of the regulatory scenario", "Quality of the model fit", "Selection of the regulative scenario without assumptions on the functional form", "Analysis of Total RNA without Nascent (INSPEcT-)", "Modeling of the rates with constant, sigmoid and impulse functions", "Confidence intervals estimation and model quality", "Performance evaluation with simulated data", "Generate simulated data with sigmoid and impulsive rates", "Generate simulated data with oscillatory rates", "Non default parameters for modeling and model selection", "Analysis of RNA dynamics in steady state RNA-seq data", "Analysis of Total and Nascent RNA", "Analysis of Total without Nascent RNA", "Wrap-up functions: running INSPEcT with a single command line", "Pipeline from BAM files", "Pipeline from PCR quantifications", "About this document", "References" ], "created": "2019-09-23 15:33:37", "modified": "2020-04-08 15:16:50", "commits": 8 }, { "source": "INSPEcT_GUI.rmd", "filename": 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