tigre-package	tigre-package
baseloglikelihoods	scoreList-class
baseloglikelihoods,scoreList-method	scoreList-class
baseloglikelihoods<-	scoreList-class
baseloglikelihoods<-,scoreList,numeric-method	scoreList-class
boundedTransform	expTransform
c,scoreList-method	scoreList-class
CGoptim	SCGoptim
cgpdisimExpandParam	modelExpandParam
cgpdisimExtractParam	modelExtractParam
cgpdisimGradient	modelGradient
cgpdisimLogLikeGradients	modelGradient
cgpdisimLogLikelihood	modelGradient
cgpdisimObjective	modelGradient
cgpdisimUpdateProcesses	modelExpandParam
cgpsimExpandParam	modelExpandParam
cgpsimExtractParam	modelExtractParam
cgpsimGradient	modelGradient
cgpsimLogLikeGradients	modelGradient
cgpsimLogLikelihood	modelGradient
cgpsimObjective	modelGradient
cgpsimOptimise	SCGoptim
cgpsimUpdateProcesses	modelExpandParam
cmpndKernCompute	kernCompute
cmpndKernDiagCompute	kernCompute
cmpndKernDiagGradX	kernDiagGradX
cmpndKernDisplay	modelDisplay
cmpndKernExpandParam	modelExpandParam
cmpndKernExtractParam	modelExtractParam
cmpndKernGradient	kernGradient
cmpndKernGradX	kernDiagGradX
cmpndKernParamInit	kernCreate
datasetName	scoreList-class
datasetName,scoreList-method	scoreList-class
datasetName<-	scoreList-class
datasetName<-,scoreList,character-method	scoreList-class
disimKernCompute	kernCompute
disimKernDiagCompute	kernCompute
disimKernDisplay	modelDisplay
disimKernExpandParam	modelExpandParam
disimKernExtractParam	modelExtractParam
disimKernGradient	kernGradient
disimKernParamInit	kernCreate
disimXdisimKernCompute	kernCompute
disimXdisimKernGradient	kernGradient
disimXrbfKernCompute	kernCompute
disimXrbfKernGradient	kernGradient
disimXsimKernCompute	kernCompute
disimXsimKernGradient	kernGradient
drosophila_gpsim_fragment	drosophila_gpsim_fragment
drosophila_mmgmos_fragment	drosophila_mmgmos_fragment
experimentSet	scoreList-class
experimentSet,scoreList-method	scoreList-class
experimentSet<-	scoreList-class
experimentSet<-,scoreList,character-method	scoreList-class
export.scores	export
ExpressionTimeSeries	ExpressionTimeSeries-class
ExpressionTimeSeries-class	ExpressionTimeSeries-class
expTransform	expTransform
gammaPriorExpandParam	modelExpandParam
gammaPriorExtractParam	modelExtractParam
gammaPriorGradient	modelGradient
gammaPriorLogProb	modelGradient
gammaPriorParamInit	kernCreate
generateModels	generateModels
genes	scoreList-class
genes,scoreList-method	scoreList-class
genes<-	scoreList-class
genes<-,scoreList,list-method	scoreList-class
gpdisimCreate	gpsimCreate
gpdisimDisplay	modelDisplay
gpdisimExpandParam	modelExpandParam
gpdisimExtractParam	modelExtractParam
gpdisimGradient	modelGradient
gpdisimLogLikeGradients	modelGradient
gpdisimLogLikelihood	modelGradient
gpdisimObjective	modelGradient
gpdisimUpdateProcesses	modelExpandParam
GPLearn	GPLearn
GPModel	GPModel-class
GPModel-class	GPModel-class
GPPlot	GPPlot
GPRankTargets	GPRankTargets
GPRankTFs	GPRankTargets
gpsimCreate	gpsimCreate
gpsimDisplay	modelDisplay
gpsimExpandParam	modelExpandParam
gpsimExtractParam	modelExtractParam
gpsimGradient	modelGradient
gpsimLogLikeGradients	modelGradient
gpsimLogLikelihood	modelGradient
gpsimObjective	modelGradient
gpsimUpdateProcesses	modelExpandParam
initialize,ExpressionTimeSeries-method	ExpressionTimeSeries-class
initialize,GPModel-method	GPModel-class
invgammaPriorExpandParam	modelExpandParam
invgammaPriorExtractParam	modelExtractParam
invgammaPriorGradient	modelGradient
invgammaPriorLogProb	modelGradient
invgammaPriorParamInit	kernCreate
is.GPModel	GPModel-class
is.GPModel,GPModel-method	GPModel-class
kernCompute	kernCompute
kernCreate	kernCreate
kernDiagCompute	kernCompute
kernDiagGradX	kernDiagGradX
kernDisplay	modelDisplay
kernExpandParam	modelExpandParam
kernExtractParam	modelExtractParam
kernGradient	kernGradient
kernGradX	kernDiagGradX
kernParamInit	kernCreate
kernPriorGradient	modelGradient
kernPriorLogProb	modelGradient
knownTargets	scoreList-class
knownTargets,scoreList-method	scoreList-class
knownTargets<-	scoreList-class
knownTargets<-,scoreList,character-method	scoreList-class
length,scoreList-method	scoreList-class
lnDiffErfs	lnDiffErfs
loglikelihoods	scoreList-class
loglikelihoods,scoreList-method	scoreList-class
loglikelihoods<-	scoreList-class
loglikelihoods<-,scoreList,numeric-method	scoreList-class
mlpKernCompute	kernCompute
mlpKernDiagGradX	kernDiagGradX
mlpKernExpandParam	modelExpandParam
mlpKernExtractParam	modelExtractParam
mlpKernGradient	kernGradient
mlpKernGradX	kernDiagGradX
mlpKernParamInit	kernCreate
modelArgs	scoreList-class
modelArgs,scoreList-method	scoreList-class
modelArgs<-	scoreList-class
modelArgs<-,scoreList,list-method	scoreList-class
modelDisplay	modelDisplay
modelExpandParam	modelExpandParam
modelExtractParam	modelExtractParam
modelGradient	modelGradient
modelLogLikelihood	modelGradient
modelObjective	modelGradient
modelOptimise	SCGoptim
modelStruct	GPModel-class
modelStruct,GPModel-method	GPModel-class
modelStruct<-	GPModel-class
modelStruct<-,GPModel,list-method	GPModel-class
modelTieParam	modelTieParam
modelType	GPModel-class
modelType,GPModel-method	GPModel-class
modelUpdateProcesses	modelExpandParam
multiKernCompute	kernCompute
multiKernDiagCompute	kernCompute
multiKernDisplay	modelDisplay
multiKernExpandParam	modelExpandParam
multiKernExtractParam	modelExtractParam
multiKernGradient	kernGradient
multiKernParamInit	kernCreate
optimiDefaultConstraint	optimiDefaultConstraint
optimiDefaultOptions	SCGoptim
params	scoreList-class
params,scoreList-method	scoreList-class
params<-	scoreList-class
params<-,scoreList,list-method	scoreList-class
plotTimeseries	plotTimeseries
priorCreate	kernCreate
priorExpandParam	modelExpandParam
priorExtractParam	modelExtractParam
priorGradient	modelGradient
priorLogProb	modelGradient
priorParamInit	kernCreate
processData	processData
processRawData	processData
rbfKernCompute	kernCompute
rbfKernDiagCompute	kernCompute
rbfKernDisplay	modelDisplay
rbfKernExpandParam	modelExpandParam
rbfKernExtractParam	modelExtractParam
rbfKernGradient	kernGradient
rbfKernParamInit	kernCreate
SCGoptim	SCGoptim
scoreList	scoreList-class
scoreList-class	scoreList-class
sharedModel	scoreList-class
sharedModel,scoreList-method	scoreList-class
sharedModel<-	scoreList-class
sharedModel<-,scoreList,list-method	scoreList-class
show,GPModel-method	GPModel-class
show,scoreList-method	scoreList-class
sigmoidTransform	expTransform
simKernCompute	kernCompute
simKernDiagCompute	kernCompute
simKernDisplay	modelDisplay
simKernExpandParam	modelExpandParam
simKernExtractParam	modelExtractParam
simKernGradient	kernGradient
simKernParamInit	kernCreate
simXrbfKernCompute	kernCompute
simXrbfKernGradient	kernGradient
simXsimKernCompute	kernCompute
simXsimKernGradient	kernGradient
sort,scoreList-method	scoreList-class
TF	scoreList-class
TF,scoreList-method	scoreList-class
TF<-	scoreList-class
TF<-,scoreList,character-method	scoreList-class
tigre	tigre-package
translateKernCompute	kernCompute
translateKernDiagCompute	kernCompute
translateKernExpandParam	modelExpandParam
translateKernExtractParam	modelExtractParam
translateKernGradient	kernGradient
translateKernParamInit	kernCreate
var.exprs	ExpressionTimeSeries-class
var.exprs,ExpressionTimeSeries-method	ExpressionTimeSeries-class
var.exprs<-	ExpressionTimeSeries-class
var.exprs<-,ExpressionTimeSeries-method	ExpressionTimeSeries-class
whiteKernCompute	kernCompute
whiteKernDiagCompute	kernCompute
whiteKernDisplay	modelDisplay
whiteKernExpandParam	modelExpandParam
whiteKernExtractParam	modelExtractParam
whiteKernGradient	kernGradient
whiteKernParamInit	kernCreate
whiteXwhiteKernCompute	kernCompute
whiteXwhiteKernGradient	kernGradient
write.scores	scoreList-class
write.scores,scoreList-method	scoreList-class
[,scoreList,ANY-method	scoreList-class
[,scoreList-method	scoreList-class
