INSPEcT: Analysis of 4sU-seq and RNA-seq time-course data

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.

AuthorStefano de Pretis
Date of publicationNone
MaintainerStefano de Pretis <ste.depo@gmail.com>
LicenseGPL-2
Version1.4.0

View on Bioconductor

Man pages

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

Functions

AIC-INSPEcT-method Man page
AIC,INSPEcT-method Man page
AIC,INSPEcT_model-method Man page
chisqmodel Man page
chisqmodel,INSPEcT-method Man page
chisqmodel,INSPEcT_model-method Man page
chisqtest Man page
chisqtest,INSPEcT-method Man page
chisqtest,INSPEcT_model-method Man page
combine Man page
combine,INSPEcT,INSPEcT-method Man page
compareSteady Man page
compareSteady,INSPEcT,INSPEcT-method Man page
degradation Man page
degradation,INSPEcT_diffsteady-method Man page
dim,INSPEcT-method Man page
Extract Man page
featureNames<-,INSPEcT-method Man page
featureNames,INSPEcT-method Man page
geneClass Man page
geneClass,INSPEcT-method Man page
geneClass,INSPEcT_model-method Man page
getModel Man page
getModel<- Man page
getModel<-,INSPEcT-method Man page
getModel,INSPEcT-method Man page
inHeatmap Man page
inHeatmap,INSPEcT-method Man page
INSPEcT Man page
[,INSPEcT,ANY,ANY-method Man page
INSPEcT-class Man page
INSPEcT_diffsteady-class Man page
[,INSPEcT_model,ANY,ANY-method Man page
INSPEcT_model-class Man page
INSPEcT-package Man page
labeledSF Man page
labeledSF,INSPEcT-method Man page
llrtests Man page
llrtests<- Man page
llrtests<-,INSPEcT-method Man page
llrtests,INSPEcT-method Man page
llrtests<-,INSPEcT_model-method Man page
llrtests,INSPEcT_model-method Man page
logLik Man page
logLik,INSPEcT-method Man page
logLik,INSPEcT_model-method Man page
makeModelRates Man page
makeModelRates,INSPEcT-method Man page
makeModelRates,INSPEcT_model-method Man page
makeRPKMs Man page
makeSimDataset Man page
makeSimDataset,INSPEcT_model-method Man page
makeSimModel Man page
makeSimModel,INSPEcT-method Man page
modelingParams Man page
modelingParams<- Man page
modelingParams<-,INSPEcT-method Man page
modelingParams,INSPEcT-method Man page
modelRates Man page
modelRates,INSPEcT-method Man page
modelSelection Man page
modelSelection<- Man page
modelSelection<-,INSPEcT-method Man page
modelSelection,INSPEcT-method Man page
modelSelection<-,INSPEcT_model-method Man page
modelSelection,INSPEcT_model-method Man page
mycerIds10 Man page
newINSPEcT Man page
nGenes Man page
nGenes,INSPEcT-method Man page
nTpts Man page
nTpts,INSPEcT-method Man page
plotGene Man page
plotGene,INSPEcT-method Man page
plotMA Man page
plotMA,INSPEcT_diffsteady-method Man page
processing Man page
processing,INSPEcT_diffsteady-method Man page
ratePvals Man page
ratePvals,INSPEcT-method Man page
ratePvals,INSPEcT_model-method Man page
ratesFirstGuess Man page
ratesFirstGuess,INSPEcT-method Man page
ratesFirstGuessVar Man page
ratesFirstGuessVar,INSPEcT-method Man page
removeModel Man page
removeModel,INSPEcT-method Man page
rocCurve Man page
rocCurve,INSPEcT_model,INSPEcT-method Man page
rocCurve,INSPEcT_model,INSPEcT_model-method Man page
rocThresholds Man page
rocThresholds,INSPEcT_model,INSPEcT-method Man page
rocThresholds,INSPEcT_model,INSPEcT_model-method Man page
rpkms Man page
sfPlot Man page
sfPlot,INSPEcT-method Man page
show,INSPEcT_diffsteady-method Man page
show,INSPEcT-method Man page
show,INSPEcT_model-method Man page
simData1rep Man page
simData3rep Man page
simRates Man page
split Man page
split,INSPEcT,ANY-method Man page
synthesis Man page
synthesis,INSPEcT_diffsteady-method Man page
testingParams Man page
thresholds Man page
thresholds<- Man page
thresholds<-,INSPEcT-method Man page
thresholds,INSPEcT-method Man page
thresholds<-,INSPEcT_model-method Man page
thresholds,INSPEcT_model-method Man page
totalSF Man page
totalSF,INSPEcT-method Man page
tpts Man page
tpts,INSPEcT-method Man page
UCSC_mm9_genes_exons Man page
UCSC_mm9_genes_introns Man page
viewModelRates Man page
viewModelRates,INSPEcT-method Man page

Files

INSPEcT/DESCRIPTION
INSPEcT/NAMESPACE
INSPEcT/R
INSPEcT/R/AllClasses.R INSPEcT/R/AllGenerics.R INSPEcT/R/AllInternalFunctions.R INSPEcT/R/Extract-methods.R INSPEcT/R/chisqtest-methods.R INSPEcT/R/dataDocumentation.R INSPEcT/R/geneClass-methods.R INSPEcT/R/getModel-methods.R INSPEcT/R/inHeatmap-methods.R INSPEcT/R/logLik-methods.R INSPEcT/R/makeModelRates-methods.R INSPEcT/R/makeRPKMs-functions.R INSPEcT/R/makeSimDataset-methods.R INSPEcT/R/makeSimModel-methods.R INSPEcT/R/modelRates-methods.R INSPEcT/R/modelingParams-methods.R INSPEcT/R/newINSPEcT-functions.R INSPEcT/R/plotGene-methods.R INSPEcT/R/ratePvals-methods.R INSPEcT/R/ratesFirstGuess-methods.R INSPEcT/R/rocCurve-methods.R INSPEcT/R/rocThresholds-methods.R INSPEcT/R/sfPlot-methods.R INSPEcT/R/show-methods.R INSPEcT/R/steady-state-methods.R INSPEcT/R/testingParams-methods.R INSPEcT/R/viewModelRates-methods.R
INSPEcT/build
INSPEcT/build/vignette.rds
INSPEcT/data
INSPEcT/data/datalist
INSPEcT/data/mycerIds10.RData
INSPEcT/data/rpkms.RData
INSPEcT/data/simData1rep.RData
INSPEcT/data/simData3rep.RData
INSPEcT/data/simData3rep_2.RData
INSPEcT/data/simRates.RData
INSPEcT/inst
INSPEcT/inst/CITATION
INSPEcT/inst/NEWS
INSPEcT/inst/doc
INSPEcT/inst/doc/INSPEcT.R
INSPEcT/inst/doc/INSPEcT.Rnw
INSPEcT/inst/doc/INSPEcT.pdf
INSPEcT/inst/extdata
INSPEcT/inst/extdata/4sURNA_0h.bam
INSPEcT/inst/extdata/totalRNA_0h.bam
INSPEcT/man
INSPEcT/man/AIC-INSPEcT-method.Rd INSPEcT/man/Extract.Rd INSPEcT/man/INSPEcT-class.Rd INSPEcT/man/INSPEcT.Rd INSPEcT/man/INSPEcT_diffsteady-class.Rd INSPEcT/man/INSPEcT_model-class.Rd INSPEcT/man/UCSC_mm9_genes_exons.Rd INSPEcT/man/UCSC_mm9_genes_introns.Rd INSPEcT/man/chisqmodel.Rd INSPEcT/man/chisqtest.Rd INSPEcT/man/combine.Rd INSPEcT/man/compareSteady.Rd INSPEcT/man/dim-INSPEcT-method.Rd INSPEcT/man/featureNames-INSPEcT-method.Rd INSPEcT/man/geneClass.Rd INSPEcT/man/getModel.Rd INSPEcT/man/inHeatmap.Rd INSPEcT/man/labeledSF.Rd INSPEcT/man/logLik.Rd INSPEcT/man/makeModelRates.Rd INSPEcT/man/makeRPKMs.Rd INSPEcT/man/makeSimDataset.Rd INSPEcT/man/makeSimModel.Rd INSPEcT/man/modelRates.Rd INSPEcT/man/modelingParams.Rd INSPEcT/man/mycerIds10.Rd INSPEcT/man/nGenes.Rd INSPEcT/man/nTpts.Rd INSPEcT/man/newINSPEcT.Rd INSPEcT/man/plotGene.Rd INSPEcT/man/plotMA.Rd INSPEcT/man/ratePvals.Rd INSPEcT/man/ratesFirstGuess.Rd INSPEcT/man/ratesFirstGuessVar.Rd INSPEcT/man/removeModel.Rd INSPEcT/man/rocCurve.Rd INSPEcT/man/rocThresholds.Rd INSPEcT/man/rpkms.Rd INSPEcT/man/sfPlot.Rd INSPEcT/man/simData1rep.Rd INSPEcT/man/simData3rep.Rd INSPEcT/man/simRates.Rd INSPEcT/man/split.Rd INSPEcT/man/testingParams.Rd INSPEcT/man/totalSF.Rd INSPEcT/man/tpts.Rd INSPEcT/man/viewModelRates.Rd
INSPEcT/vignettes
INSPEcT/vignettes/INSPEcT.Rnw
INSPEcT/vignettes/pipeline.png

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