ste-depo/INSPEcT
Modeling RNA synthesis, processing and degradation with RNA-seq data

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468
Source code
44
Man pages
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ste-depo/INSPEcT: Modeling RNA synthesis, processing and degradation with RNA-seq data
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API

API for ste-depo/INSPEcT
Modeling RNA synthesis, processing and degradation with RNA-seq data

Global functions
.D2impulseModel Source code
.D2sigmoidModel Source code
.DimpulseModel Source code
.DprematureVKK_Der Source code
.DprematureVKV_Der Source code
.DprematureVVK_Der Source code
.DprematureVVV_Der Source code
.DsigmoidModel Source code
.busyIndicator Source code
.chooseModel Source code
.emptyGene Source code
.inspect.engine_Derivative_Nascent Source code
.inspect.engine_Derivative_Nascent_sdp Source code
.inspect.engine_Derivative_NoNascent Source code
.inspect.engine_Integrative_Nascent Source code
.inspect.engine_Integrative_Nascent_sdp Source code
.inspect.engine_Integrative_NoNascent Source code
.makeEmptyModel Source code
.makeEmptySimpleModel Source code
.makeModel Source code
.makeModel_Derivative Source code
.makeSimData Source code
.makeSimpleModel Source code
.polynomialModel Source code
.rxnrate Source code
.rxnrateSimple Source code
.which.quantile Source code
AIC,INSPEcT-method Man page
AIC,INSPEcT_model-method Man page
AIC-INSPEcT-method Man page
AIC_internal Source code
Extract Man page
INSPEcT Man page
INSPEcT-class Man page
INSPEcT-shinyApps Man page
INSPEcTGUIshinyAppServer Source code
INSPEcT_diffsteady-class Man page
INSPEcT_model-class Man page
INSPEcT_steadyNoNascent-class Man page
PTratio Man page
PTratio,INSPEcT_steadyNoNascent-method Man page
PTreg Man page
PTreg,INSPEcT_steadyNoNascent-method Man page
ProcessingRateDelayshinyAppServer Source code
RNAdynamics Source code
RNAdynamicsAppMake Source code
RNAdynamicsAppMakeConfInt Source code
RNAdynamicsAppPlot Source code
RNAdynamicsDDP Source code
RNAdynamicsFromPreex 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
[,INSPEcT_steadyNoNascent,ANY,ANY,ANY-method Man page
allcounts Man page
brown_method Source code
brown_method_mask Source code
calculateDelta Man page
calculateDelta,INSPEcT-method Man page
calculateRatePvals Man page
calculateRatePvals,INSPEcT-method Man page
calculateTau Man page
calculateTau,INSPEcT-method Man page
calculate_rates_pvalues Source code
checkINSPEcTObjectversion Source code
chisqFunction Source code Source code
chisqmodel Man page
chisqmodel,INSPEcT-method Man page
chisqmodelfun Source code
chisqtest Man page
chisqtest,INSPEcT-method Man page
chisqtest,INSPEcT_model-method Man page
chisqtest_internal Source code
classificationFunction Source code
classify_rates_from_priors_4sU_v5 Source code
classify_rates_from_priors_v5 Source code
combine Man page
combine,INSPEcT,INSPEcT-method Man page
compareSteady Man page
compareSteady,INSPEcT-method Man page
compareSteadyNoNascent Man page
compareSteadyNoNascent,INSPEcT_steadyNoNascent-method Man page
computeConfidenceIntervals Man page
computeConfidenceIntervals,INSPEcT-method Man page
compute_ci_Derivative_Nascent Source code
compute_ci_Integrative_Nascent Source code
constantModel Source code
constantModelRNApp Source code
convergence Man page
convergence,INSPEcT-method Man page
coordinatesAIC Source code
correlationPlot Man page
correlationPlot,INSPEcT_model,INSPEcT-method Man page
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
deltaylim Source code
derivative_solution Source code
derivative_solution_no_nascent Source code
deterministic_simulation Source code
dim,INSPEcT-method Man page
errorKKK_Der Source code
errorKKK_Int Source code
errorKKK_Int_NoNascent Source code
errorKKK_ddpFALSE Source code
errorKKK_ddpTRUE Source code
errorKKV_Der Source code
errorKKV_Der_App Source code
errorKKV_Int Source code
errorKKV_Int_NoNascent Source code
errorKKV_ddpFALSE Source code
errorKKV_ddpTRUE Source code
errorKK_ddpTRUE Source code
errorKVK_Der Source code
errorKVK_Der_App Source code
errorKVK_Int Source code
errorKVK_Int_NoNascent Source code
errorKVK_ddpFALSE Source code
errorKVK_ddpTRUE Source code
errorKVV_Der Source code
errorKVV_Der_App Source code
errorKVV_Int 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
errorOptim Source code
errorVKK_Der Source code
errorVKK_Der_NoNascent Source code
errorVKK_Int Source code
errorVKK_Int_NoNascent Source code
errorVKK_ddpFALSE Source code
errorVKK_ddpTRUE Source code
errorVKV_Der Source code
errorVKV_Der_NoNascent Source code
errorVKV_Int Source code
errorVKV_Int_NoNascent Source code
errorVKV_ddpFALSE Source code
errorVKV_ddpTRUE Source code
errorVK_ddpTRUE Source code
errorVVK_Der Source code
errorVVK_Der_NoNascent Source code
errorVVK_Int Source code
errorVVK_Int_NoNascent Source code
errorVVK_ddpFALSE Source code
errorVVK_ddpTRUE Source code
errorVVV_Der Source code
errorVVV_Der_NoNascent Source code
errorVVV_Int 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
estimate_priors Source code
expressionData_integrativeModels Source code
expressionProfilesFromPiecedFunctions Source code
expressionProfilesFromPiecedFunctionsManyNA Source code
fGamma Source code
fLint Source code
featureNames,INSPEcT-method Man page
featureNames,INSPEcT_diffsteady-method Man page
featureNames<-,INSPEcT-method Man page
featureWidths Man page
findttpar Source code
firstStepError_NoNascent Source code
firstStep_NoNascent Source code
fitSmooth Source code
fromSigmoidToImpulse Source code
geneClass Man page
geneClass,INSPEcT-method Man page
geneClass,INSPEcT_diffsteady-method Man page
geneClass,INSPEcT_model-method Man page
geneClassInternal Source code
generateOscillatoryParams Source code
generateParamsShift Source code
genericError_Int Source code
getK1params Source code
getK2params Source code
getK3params Source code
grepLogic Source code
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
inspectFromBAM Man page Source code
inspectFromPCR Man page Source code
k1KKK_Der Source code
k1KKK_Int Source code
k1KKK_Int_NoNascent Source code
k1KKV_Der Source code
k1KKV_Der_App Source code
k1KVK_Der Source code
k1KVK_Der_App Source code
k1KVV_Der Source code
k1KVV_Der_App Source code
k1VKK_Der Source code
k1VKK_Der_NoNascent Source code
k1VKV_Der Source code
k1VKV_Der_NoNascent Source code
k1VVK_Der Source code
k1VVK_Der_NoNascent Source code
k1VVV_Der Source code
k1VVV_Der_NoNascent Source code
k2KKK_Der Source code
k2KKK_Int Source code
k2KKV_Der Source code
k2KKV_Der_App Source code
k2KVK_Der Source code
k2KVK_Der_App Source code
k2KVV_Der Source code
k2KVV_Der_App Source code
k2VKK_Der Source code
k2VKV_Der Source code
k2VVK_Der Source code
k2VVV_Der Source code
k3KKK_Der Source code
k3KKK_Int Source code
k3KKV_Der Source code
k3KKV_Der_App Source code
k3KVK_Der Source code
k3KVK_Der_App Source code
k3KVV_Der Source code
k3KVV_Der_App Source code
k3VKK_Der Source code
k3VKV_Der Source code
k3VVK_Der Source code
k3VVV_Der Source code
k_score_fun Source code
labeledSF Man page
labeledSF,INSPEcT-method Man page
libsizes Man page
lin2logPar Source code
lineCoefficients_NoNascent Source code
log2linPar Source code
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
logLik_internal Source code
logLikelihoodCIerror Source code
logLikelihoodCIerror4sU_NF Source code
logLikelihoodCIerror_NF Source code
logLikelihoodFunction Source code Source code
logLikelihood_derivativeModels Source code
logLikelihood_integrativeModels 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
makeModelRates Man page
makeModelRates,INSPEcT-method Man page
makeModelRates,INSPEcT_model-method Man page
makeOscillatorySimModel Man page
makeOscillatorySimModel,INSPEcT-method Man page
makeSimDataset Man page
makeSimDataset,INSPEcT_model-method Man page
makeSimModel Man page
makeSimModel,INSPEcT-method Man page
matchSeqnames Source code
matrixColNorm Source code
mature Man page
mature,INSPEcT_steadyNoNascent-method Man page
matureKKK_Der Source code
matureKKV_Der Source code
matureKVK_Der Source code
matureKVV_Der Source code
matureVKK_Der Source code
matureVKV_Der Source code
matureVVK_Der Source code
matureVVV_Der Source code
matureVar Man page
matureVar,INSPEcT_steadyNoNascent-method Man page
mcsapply Source code
mirror_hig Source code
mirror_low Source code
modelChisqMatureRNA Source code
modelRates Man page
modelRates,INSPEcT-method Man page
modelRatesNF Man page
modelRatesNF,INSPEcT-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
modeling_report Source code
nGenes Man page
nGenes,INSPEcT-method Man page
nTpts Man page
nTpts,INSPEcT-method Man page
newINSPEcT Man page Source code
newPointer Source code
optimParamsMatureRNA Source code
optimPositive Source code
oscillatoryModel Source code
output_pars Source code
perturbedLogLikelihood4sU_NF Source code
perturbedLogLikelihood_NF Source code
piecedFunctionLogLikelihood Source code
piecedFunctionLogLikelihood4sU Source code
piecedFunctionLogLikelihoodManyNA Source code
piecedFunctionLogLikelihoodManyNA4sU Source code
plotGene Man page
plotGene,INSPEcT-method Man page
plotMA Man page
plotMA,INSPEcT_diffsteady-method Man page
plotPMgene Man page
plotPMgene,INSPEcT_steadyNoNascent-method Man page
plotPMtrend Man page
plotPMtrend,INSPEcT_steadyNoNascent-method Man page
plotSingleRNADynamic Source code
premature Man page
premature,INSPEcT_steadyNoNascent-method Man page
prematureKKK_Der Source code
prematureKKK_Int_NoNascent Source code
prematureKKV_Der Source code
prematureKKV_Der_App Source code
prematureKVK_Der Source code
prematureKVK_Der_App Source code
prematureKVV_Der Source code
prematureKVV_Der_App Source code
prematureVKK_Der Source code
prematureVKK_Der_NoNascent Source code
prematureVKV_Der Source code
prematureVKV_Der_NoNascent Source code
prematureVVK_Der Source code
prematureVVK_Der_NoNascent Source code
prematureVVV_Der Source code
prematureVVV_Der_NoNascent Source code
prematureVar Man page
prematureVar,INSPEcT_steadyNoNascent-method Man page
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
quantifyExpressionsFromBWs Man page Source code
quantifyExpressionsFromTrAbundance Man page Source code
quantifyExpressionsFromTrCounts Man page Source code
ratePvals Man page
ratePvals,INSPEcT-method Man page
rate_conf_int_impute Source code
rate_var_p Source code
ratesFirstGuess Man page
ratesFirstGuess,INSPEcT-method Man page
ratesFirstGuessVar Man page
ratesFirstGuessVar,INSPEcT-method Man page
rates_derivativeModels Source code
rates_from_napars Source code
rates_integrativeModels Source code
reconvert_gene_classes Source code
removeModel Man page
removeModel,INSPEcT-method Man page
rocCurve Man page
rocCurve,INSPEcT_model,INSPEcT-method Man page
rocThresholds Man page
rocThresholds,INSPEcT_model,INSPEcT-method Man page
runINSPEcTGUI Man page Source code
runProcessingRateDelay Man page Source code
rxnrateMatureRNA Source code
sampleNorm2DQuantile Source code
sampleNormQuantile Source code
score_and_par Source code
secondStepError_NoNascent Source code
setConfidenceIntervals Man page
setConfidenceIntervals,INSPEcT-method Man page
shinyProcessingDelayPlot Source code
show,INSPEcT-method Man page
show,INSPEcT_diffsteady-method Man page
show,INSPEcT_model-method Man page
show,INSPEcT_steadyNoNascent-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
sq.median.resids Source code
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
systemSolution_Simple Source code
tau_fun Source code
timetransf Source code
timetransf_NoNascent Source code
timetransf_inv Source code
tpts Man page
tpts,INSPEcT-method Man page
viewConfidenceIntervals Man page
viewConfidenceIntervals,INSPEcT-method Man page
viewModelRates Man page
viewModelRates,INSPEcT-method Man page
ste-depo/INSPEcT documentation built on Oct. 3, 2020, 9:14 p.m.

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