API for 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-shinyApps Man page
INSPEcT_diffsteady-class Man page
INSPEcT_model-class Man page
RNAdynamics Source code
RNAdynamicsAppPlot Source code
RNAdynamicsDDP Source code
RNAdynamicsSimple Source code
RNAdynamicsSimpleDDP Source code
RNAdynamics_NoNascent Source code
[,INSPEcT,ANY,ANY,ANY-method Man page
[,INSPEcT_diffsteady,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
calculateDelta Man page
calculateDelta,INSPEcT-method Man page
calculateTau Man page
calculateTau,INSPEcT-method Man page
chisqFunction 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-method Man page
compareSteadyNoNascent Man page
compareSteadyNoNascent,INSPEcT-method Man page
constantModel Source code
constantModelRNApp Source code
convert_gene_classes Source code
countVar2expressions Source code
counts2expressions Source code
createInspectObject Source code
define_parameter_ranges Source code
degradation Man page
degradation,INSPEcT_diffsteady-method Man page
delta_fun Source code
deterministic_simulation Source code
dim,INSPEcT-method Man page
emptyGene Source code
errorKKK_Int_NoNascent Source code
errorKKK_ddpFALSE Source code
errorKKK_ddpTRUE Source code
errorKKV_Int_NoNascent Source code
errorKKV_ddpFALSE Source code
errorKKV_ddpTRUE Source code
errorKK_ddpTRUE Source code
errorKVK_Int_NoNascent Source code
errorKVK_ddpFALSE Source code
errorKVK_ddpTRUE Source code
errorKVV_Int_NoNascent Source code
errorKVV_ddpFALSE Source code
errorKVV_ddpTRUE Source code
errorKV_ddpTRUE Source code
errorK_K_ddpFALSE Source code
errorK_V_ddpFALSE Source code
errorVKK_Der_NoNascent Source code
errorVKK_Int_NoNascent Source code
errorVKK_ddpFALSE Source code
errorVKK_ddpTRUE Source code
errorVKV_Der_NoNascent Source code
errorVKV_Int_NoNascent Source code
errorVKV_ddpFALSE Source code
errorVKV_ddpTRUE Source code
errorVK_ddpTRUE Source code
errorVVK_Der_NoNascent Source code
errorVVK_Int_NoNascent Source code
errorVVK_ddpFALSE Source code
errorVVK_ddpTRUE Source code
errorVVV_Der_NoNascent Source code
errorVVV_Int_NoNascent Source code
errorVVV_ddpFALSE Source code
errorVVV_ddpTRUE Source code
errorVV_ddpTRUE Source code
errorV_K_ddpFALSE Source code
errorV_V_ddpFALSE Source code
featureNames,INSPEcT-method Man page
featureNames,INSPEcT_diffsteady-method Man page
featureNames<-,INSPEcT-method Man page
featureWidths 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
hrtime Source code
impulseModel Source code
impulseModelRNApp 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
libsizes 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
logLikKKK_ddpFALSE Source code
logLikKKK_ddpTRUE Source code
logLikKKV_ddpFALSE Source code
logLikKKV_ddpTRUE Source code
logLikKK_ddpTRUE Source code
logLikKVK_ddpFALSE Source code
logLikKVK_ddpTRUE Source code
logLikKVV_ddpFALSE Source code
logLikKVV_ddpTRUE Source code
logLikKV_ddpTRUE Source code
logLikK_K_ddpFALSE Source code
logLikK_V_ddpFALSE Source code
logLikRatioTest Source code
logLikRatioTestInscpectModels Source code
logLikVKK_ddpFALSE Source code
logLikVKK_ddpTRUE Source code
logLikVKV_ddpFALSE Source code
logLikVKV_ddpTRUE Source code
logLikVK_ddpTRUE Source code
logLikVVK_ddpFALSE Source code
logLikVVK_ddpTRUE Source code
logLikVVV_ddpFALSE Source code
logLikVVV_ddpTRUE Source code
logLikVV_ddpTRUE Source code
logLikV_K_ddpFALSE Source code
logLikV_V_ddpFALSE 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
m_t_complete Source code
m_t_simple 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
matrixColNorm Source code
mcsapply Source code
modelChisqMatureRNA 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
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
nspect.engine_Derivative_NoNascent Source code
nspect.engine_Integrative_NoNascent Source code
optimParamsMatureRNA 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
priorRates_ddpTRUE Source code
processing Man page
processing,INSPEcT_diffsteady-method Man page
processingDelay Man page
processingDelay,INSPEcT-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
ratesFirstGuess Man page
ratesFirstGuess,INSPEcT-method Man page
ratesFirstGuessVar Man page
ratesFirstGuessVar,INSPEcT-method Man page
reconvert_gene_classes Source code
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
runProcessingRateDelay Man page Source code
runRNAdynamics Man page Source code
rxnrate Source code
rxnrateMatureRNA Source code
rxnrateSimple Source code
secondStepError_NoNascent Source code
sfPlot Man page
sfPlot,INSPEcT-method Man page
shinyProcessingDelayPlot Source code
show,INSPEcT-method Man page
show,INSPEcT_diffsteady-method Man page
show,INSPEcT_model-method Man page
sigmoidModel Source code
sigmoidModelRNApp Source code
simData3rep_Nascent Man page
simData3rep_NoNascent Man page
simData4rep_Nascent Man page
simData4rep_NoNascent Man page
simplepriorRates_ddpTRUE Source code
simplesys4suChisq_ddpTRUE Source code
simplesys4suLoglik_ddpTRUE Source code
simplesys4suModel_ddpTRUE Source code
smoothModel Source code
split Man page
split,INSPEcT,ANY-method Man page
standardCurveFitFunction Source code
synthesis Man page
synthesis,INSPEcT_diffsteady-method Man page
sys4suChisq_ddpFALSE Source code
sys4suChisq_ddpTRUE Source code
sys4suLoglik_ddpFALSE Source code
sys4suLoglik_ddpTRUE Source code
sys4suModel_ddpFALSE Source code
sys4suModel_ddpTRUE Source code
sys4suSimpleChisq_ddpFALSE Source code
sys4suSimpleLoglik_ddpFALSE Source code
sys4suSimpleModel_ddpFALSE Source code
sysScaleChisq_ddpTRUE Source code
systemSolution Source code
tau_fun 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
time_transf_inv Source code
tpts Man page
tpts,INSPEcT-method Man page
viewModelRates Man page
viewModelRates,INSPEcT-method Man page
which.quantile Source code
INSPEcT documentation built on Dec. 25, 2018, 6 p.m.