INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and asses via modeling the rates that determines changes in mature mRNA levels.
|Author||Stefano de Pretis|
|Date of publication||None|
|Maintainer||Stefano de Pretis <email@example.com>|
AIC-INSPEcT-method: Akaike information criterion calculated for the models...
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 two...
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
geneClass: Retrieve the regulatory class for each gene
getModel: Get or replace INSPEcT_model object within INSPEcT object
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...
INSPEcT_model-class: An S4 class to represent models generated by INSPEcT
labeledSF: Accessor to the slot labeledSF of an INSPEcT object
logLik: Retrieve results of log likelihood test
makeModelRates: Calculate modeled rates and concentrations
makeRPKMs: Calculate RPKM and count values on introns and exons from...
makeSimDataset: Generate synthetic rates and concentrations
makeSimModel: Build the synthetic rates shaped on a dataset
modelingParams: Get and set number parameters for the modeling
modelRates: Launch the modeling process
mycerIds10: An INSPEcT object with evaluated and modeled rates and...
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
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...
rpkms: intron, exons RPKM values of 500 genes from 4sU-seq and...
sfPlot: A nice plot to see scaling factors used for RNA-seq and...
simData1rep: An INSPEcT object with 1000 simulated rates and concentration...
simData3rep: An INSPEcT object with 1000 simulated rates and concentration...
simRates: An INSPEcT_model object of 1000 simulated rates
split: Divide an INSPEcT Object into groups
testingParams: Get or set parameters for model test and selection
totalSF: Accessor to the slot totalSF of an INSPEcT object
tpts: Accessor to the slot tpts of an INSPEcT object
UCSC_mm9_genes_exons: A Gtf file containing exons definition of 100 genes
UCSC_mm9_genes_introns: A Gtf file containing introns definition of 100 genes
viewModelRates: Retrieve the modeled rates and concentrations