INSPEcT: Analysis of 4sU-seq and RNA-seq time-course data
Version 1.6.0

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.

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AuthorStefano de Pretis
Bioconductor views GeneRegulation RNASeq Sequencing SystemsBiology TimeCourse
Date of publicationNone
MaintainerStefano de Pretis <ste.depo@gmail.com>
LicenseGPL-2
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("INSPEcT")

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_model-method Man page
AIC-INSPEcT-method Man page
DimpulseModel Source code
DsigmoidModel Source code
Extract Man page
INSPEcT Man page
INSPEcT-class Man page
INSPEcT-package Man page
INSPEcT_diffsteady-class Man page
INSPEcT_model-class Man page
UCSC_mm9_genes_exons Man page
UCSC_mm9_genes_introns Man page
[,INSPEcT,ANY,ANY,ANY-method Man page
[,INSPEcT_model,ANY,ANY,ANY-method Man page
bestModel Source code
brown_method Source code
brown_method_mask Source code
chisq Source code
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
chooseModel Source code
combine Man page
combine,INSPEcT,INSPEcT-method Man page
compareSteady Man page
compareSteady,INSPEcT,INSPEcT-method Man page
constantModel Source code
degradation Man page
degradation,INSPEcT_diffsteady-method Man page
dim,INSPEcT-method Man page
emptyGene Source code
featureNames,INSPEcT-method Man page
featureNames<-,INSPEcT-method Man page
find_tt_par Source code
geneClass Man page
geneClass,INSPEcT-method Man page
geneClass,INSPEcT_model-method Man page
getModel Man page
getModel,INSPEcT-method Man page
getModel<- Man page
getModel<-,INSPEcT-method Man page
getRatesAndConcentrationsFromRpkms Source code
inHeatmap Man page
inHeatmap,INSPEcT-method Man page
labeledSF Man page
labeledSF,INSPEcT-method Man page
llrtests Man page
llrtests,INSPEcT-method Man page
llrtests,INSPEcT_model-method Man page
llrtests<- Man page
llrtests<-,INSPEcT-method Man page
llrtests<-,INSPEcT_model-method Man page
logLik Man page
logLik,INSPEcT-method Man page
logLik,INSPEcT_model-method Man page
logLikRatioTest Source code
logLikelihood Source code
makeEmptyModel Source code
makeEmptySimpleModel Source code
makeModel Source code
makeModelRates Man page
makeModelRates,INSPEcT-method Man page
makeModelRates,INSPEcT_model-method Man page
makeRPKMs Man page Source code
makeSimData Source code
makeSimDataset Man page
makeSimDataset,INSPEcT_model-method Man page
makeSimModel Man page
makeSimModel,INSPEcT-method Man page
makeSimpleModel Source code
modelRates Man page
modelRates,INSPEcT-method Man page
modelSelection Man page
modelSelection,INSPEcT-method Man page
modelSelection,INSPEcT_model-method Man page
modelSelection<- Man page
modelSelection<-,INSPEcT-method Man page
modelSelection<-,INSPEcT_model-method Man page
modelingParams Man page
modelingParams,INSPEcT-method Man page
modelingParams<- Man page
modelingParams<-,INSPEcT-method Man page
mpulseModel Source code
mycerIds10 Man page
nGenes Man page
nGenes,INSPEcT-method Man page
nTpts Man page
nTpts,INSPEcT-method Man page
newINSPEcT Man page Source code
newPointer Source code
nspect.engine Source code
plotGene Man page
plotGene,INSPEcT-method Man page
plotMA Man page
plotMA,INSPEcT_diffsteady-method Man page
polynomialModel Source code
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
rowVars Source code
rowVars2 Source code
rpkms Man page
rxnrate Source code
rxnrateSimple Source code
sfPlot Man page
sfPlot,INSPEcT-method Man page
show,INSPEcT-method Man page
show,INSPEcT_diffsteady-method Man page
show,INSPEcT_model-method Man page
sigmoidModel Source code
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,INSPEcT-method Man page
thresholds,INSPEcT_model-method Man page
thresholds<- Man page
thresholds<-,INSPEcT-method Man page
thresholds<-,INSPEcT_model-method Man page
time_transf Source code
totalSF Man page
totalSF,INSPEcT-method Man page
tpts Man page
tpts,INSPEcT-method Man page
viewModelRates Man page
viewModelRates,INSPEcT-method Man page
which.quantile Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/AllInternalFunctions.R
R/Extract-methods.R
R/chisqtest-methods.R
R/dataDocumentation.R
R/geneClass-methods.R
R/getModel-methods.R
R/inHeatmap-methods.R
R/logLik-methods.R
R/makeModelRates-methods.R
R/makeRPKMs-functions.R
R/makeSimDataset-methods.R
R/makeSimModel-methods.R
R/modelRates-methods.R
R/modelingParams-methods.R
R/newINSPEcT-functions.R
R/plotGene-methods.R
R/ratePvals-methods.R
R/ratesFirstGuess-methods.R
R/rocCurve-methods.R
R/rocThresholds-methods.R
R/sfPlot-methods.R
R/show-methods.R
R/steady-state-methods.R
R/testingParams-methods.R
R/viewModelRates-methods.R
build
build/vignette.rds
data
data/datalist
data/mycerIds10.RData
data/rpkms.RData
data/simData1rep.RData
data/simData3rep.RData
data/simData3rep_2.RData
data/simRates.RData
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/INSPEcT.R
inst/doc/INSPEcT.Rnw
inst/doc/INSPEcT.pdf
inst/extdata
inst/extdata/4sURNA_0h.bam
inst/extdata/totalRNA_0h.bam
man
man/AIC-INSPEcT-method.Rd
man/Extract.Rd
man/INSPEcT-class.Rd
man/INSPEcT.Rd
man/INSPEcT_diffsteady-class.Rd
man/INSPEcT_model-class.Rd
man/UCSC_mm9_genes_exons.Rd
man/UCSC_mm9_genes_introns.Rd
man/chisqmodel.Rd
man/chisqtest.Rd
man/combine.Rd
man/compareSteady.Rd
man/dim-INSPEcT-method.Rd
man/featureNames-INSPEcT-method.Rd
man/geneClass.Rd
man/getModel.Rd
man/inHeatmap.Rd
man/labeledSF.Rd
man/logLik.Rd
man/makeModelRates.Rd
man/makeRPKMs.Rd
man/makeSimDataset.Rd
man/makeSimModel.Rd
man/modelRates.Rd
man/modelingParams.Rd
man/mycerIds10.Rd
man/nGenes.Rd
man/nTpts.Rd
man/newINSPEcT.Rd
man/plotGene.Rd
man/plotMA.Rd
man/ratePvals.Rd
man/ratesFirstGuess.Rd
man/ratesFirstGuessVar.Rd
man/removeModel.Rd
man/rocCurve.Rd
man/rocThresholds.Rd
man/rpkms.Rd
man/sfPlot.Rd
man/simData1rep.Rd
man/simData3rep.Rd
man/simRates.Rd
man/split.Rd
man/testingParams.Rd
man/totalSF.Rd
man/tpts.Rd
man/viewModelRates.Rd
vignettes
vignettes/INSPEcT.Rnw
vignettes/pipeline.png
INSPEcT documentation built on May 20, 2017, 10:37 p.m.