Modeling RNA synthesis, processing and degradation with RNA-seq data

AIC-INSPEcT-method | Akaike information criterion calculated for the models... |

allcounts | A list containing mature and nascent counts for exons and... |

calculateRatePvals | Calculate a single p-value for each rate |

chisqmodel | Retrieve results of chi-squared test for the selected models |

chisqtest | Retrieve all results of chi-squared test |

combine | Combine different Objects of Class INSPEcT |

compareSteady | Generate an object of class INSPEcT_diffsteady from an object... |

compareSteadyNoNascent | Identify post-transcriptionally regulated genes from an... |

computeConfidenceIntervals | Compute confidence intervals |

convergence | Retrieve the convergence for the selected models of each gene |

correlationPlot | Display rate classification performance |

dim-INSPEcT-method | Dimensions of an Object of Class INSPEcT |

Extract | Extract Parts of an INSPEcT or an INSPEcT_model Object |

featureNames-INSPEcT-method | Gene Names Associated with an Object of Class INSPEcT |

featureWidths | Contains two variables: "exWdths" and "intWdths" containing... |

geneClass | Retrieve the regulatory class for each gene |

inHeatmap | Heatmap that represent the fold changes of all the five... |

INSPEcT | INSPEcT package |

INSPEcT-class | An S4 class to contain all rates and models generated by... |

INSPEcT_diffsteady-class | An S4 class to represent comparisons between two steady-state... |

inspectFromBAM | Wrapper function from BAM files |

inspectFromPCR | Wrapper function from PCR quantifications |

INSPEcT_model-class | An S4 class to represent models generated by INSPEcT |

INSPEcT-shinyApps | Run shiny applications contained in the package INSPEcT |

INSPEcT_steadyNoNascent-class | An S4 class to represent steady-state analysis without... |

labeledSF | Accessor to the slot labeledSF of an INSPEcT object |

libsizes | Contains two variables: "nascentLS" and "totalLS" containing... |

logLik | Retrieve results of log likelihood test |

makeModelRates | Calculate modeled rates and concentrations |

makeOscillatorySimModel | Build the synthetic rates with oscillatory pattern |

makeSimDataset | Generate synthetic rates and concentrations |

makeSimModel | Build the synthetic rates shaped on a dataset |

mature | Get mature RNA expressions from an object of class... |

matureVar | Get mature RNA expressions variances from an object of class... |

modelingParams | Get and set number parameters for the modeling |

modelRates | Launch the modeling process |

modelRatesNF | Launch the modeling process without imposing sigmoid/impulse... |

modelSelection | Visualize criteria used for rate variability |

newINSPEcT | Create a new INSPEcT object |

nGenes | Get the number of genes within the INSPEcT object |

nTpts | Get the number of time points within the INSPEcT object |

plotGene | Plot the pre-modeled and modeled profiles for one gene |

plotMA | MA-plot from base means and log fold changes |

plotPMgene | Plot the premature/mature expression of a gene and the global... |

plotPMtrend | Plot the premature/mature trend from an object of class... |

premature | Get premature RNA expressions from an object of class... |

prematureVar | Get premature RNA expressions variances from an object of... |

processingDelay | Classify genes as delayed by the processing using the delta... |

PTratio | Calculate post-transcriptional ratio from an object of class... |

PTreg | Calculate the post-transcriptional ratio from an object of... |

quantifyExpressionsFromBAMs | Evaluate introns and exons expressions from BAM or SAM files |

quantifyExpressionsFromBWs | Evaluate introns and exons expressions from BAM or SAM files |

quantifyExpressionsFromTrAbundance | Given introns and exons abundances (for example RPKMs) this... |

quantifyExpressionsFromTrCounts | Evaluates introns and exons RPKMs, per gene, from counts... |

ratePvals | Retrieve a single p-value for each rate |

ratesFirstGuess | Retrieve pre-modeling rates and concentrations |

ratesFirstGuessVar | Retrieve pre-modeling rates and concentrations variance |

removeModel | remove modelling information from INSPEcT object |

rocCurve | Display rate classification performance |

rocThresholds | Display rate classification performance with thresholds... |

setConfidenceIntervals | Set confidence intervals |

simData3rep_Nascent | An INSPEcT object with 1000 simulated rates and concentration... |

simData3rep_NoNascent | An INSPEcT object with 1000 simulated rates and concentration... |

simData4rep_Nascent | An INSPEcT object with 1000 simulated rates and concentration... |

simData4rep_NoNascent | An INSPEcT object with 1000 simulated rates and concentration... |

split | Divide an INSPEcT Object into groups |

tpts | Accessor to the slot tpts of an INSPEcT object |

viewConfidenceIntervals | Retrieve the modeled Confidence Intervals |

viewModelRates | Retrieve the modeled rates and concentrations |

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