API for ste-depo/INSPEcT
Analysis of 4sU-seq and RNA-seq time-course data

Global functions
AIC,INSPEcT-method Man page
AIC,INSPEcT_model-method Man page
AIC-INSPEcT-method Man page
D2impulseModel Source code
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
[,INSPEcT,ANY,ANY,ANY-method Man page
[,INSPEcT_model,ANY,ANY,ANY-method Man page
allcounts 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
classificationFunction Source code
combine Man page
combine,INSPEcT,INSPEcT-method Man page
compareSteady Man page
compareSteady,INSPEcT,INSPEcT,numeric,numeric-method Man page
compareSteadyNoNascent Man page Source code
constantModel Source code
countVar2expressions Source code
counts2expressions Source code
createInspectObject Source code
degradation Man page
degradation,INSPEcT_diffsteady-method Man page
dim,INSPEcT-method Man page
emptyGene Source code
errorKKK_Int_NoNascent Source code
errorKKV_Int_NoNascent Source code
errorKVK_Int_NoNascent Source code
errorKVV_Int_NoNascent Source code
errorVKK_Der_NoNascent Source code
errorVKK_Int_NoNascent Source code
errorVKV_Der_NoNascent Source code
errorVKV_Int_NoNascent Source code
errorVVK_Der_NoNascent Source code
errorVVK_Int_NoNascent Source code
errorVVV_Der_NoNascent Source code
errorVVV_Int_NoNascent Source code
featureNames,INSPEcT-method Man page
featureNames<-,INSPEcT-method Man page
find_tt_par Source code
firstStepError_NoNascent Source code
firstStep_NoNascent Source code
fitSmooth 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
impute_na_tc Source code
inHeatmap Man page
inHeatmap,INSPEcT-method Man page
inferKBetaFromIntegralWithPre Source code
inferKGammaFromIntegral Source code
k1KKK_Int_NoNascent Source code
k1VKK_Der_NoNascent Source code
k1VKV_Der_NoNascent Source code
k1VVK_Der_NoNascent Source code
k1VVV_Der_NoNascent Source code
labeledSF Man page
labeledSF,INSPEcT-method Man page
lineCoefficients_NoNascent Source code
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
logLikelihoodFunction Source code
loglikKKK_Int_NoNascent Source code
loglikKKV_Int_NoNascent Source code
loglikKVK_Int_NoNascent Source code
loglikKVV_Int_NoNascent Source code
loglikVKK_Int_NoNascent Source code
loglikVKV_Int_NoNascent Source code
loglikVVK_Int_NoNascent Source code
loglikVVV_Int_NoNascent 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
makeModel_Derivative 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
mcsapply 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
nGenes Man page
nGenes,INSPEcT-method Man page
nTpts Man page
nTpts,INSPEcT-method Man page
nascentInspObj Man page
nascentInspObj10 Man page
newINSPEcT Man page Source code
newPointer Source code
nspect.engine Source code
nspect.engine_Derivative_NoNascent Source code
nspect.engine_Integrative_NoNascent Source code
plotGene Man page
plotGene,INSPEcT-method Man page
plotMA Man page
plotMA,INSPEcT_diffsteady-method Man page
polynomialModel Source code
prematureKKK_Int_NoNascent Source code
prematureVKK_Der_NoNascent Source code
prematureVKV_Der_NoNascent Source code
prematureVVK_Der_NoNascent Source code
prematureVVV_Der_NoNascent Source code
processing Man page
processing,INSPEcT_diffsteady-method Man page
quantifyExpressionsFromBAMs Man page Source code
quantifyExpressionsFromTrAbundance Man page Source code
quantifyExpressionsFromTrCounts Man page Source code
ratePvals Man page
ratePvals,INSPEcT-method Man page
ratePvals,INSPEcT_model-method Man page
ratesAndConcentrationsNoNascent Source code
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
rxnrate Source code
rxnrateSimple Source code
secondStepError_NoNascent 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
split Man page
split,INSPEcT,ANY-method Man page
standardCurveFitFunction Source code
synthesis Man page
synthesis,INSPEcT_diffsteady-method Man page
systemSolution Source code
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
time_transf_NoNascent 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
ste-depo/INSPEcT documentation built on July 30, 2018, 12:04 p.m.