addTrail	addTrail
addTrail,SingleCellExperiment-method	addTrail
connectStates	connectStates
connectStates,SingleCellExperiment-method	connectStates
contrastTrailExpr	contrastTrailExpr
contrastTrailExpr,SingleCellExperiment-method	contrastTrailExpr
embedSamples	embedSamples
embedSamples,matrix-method	embedSamples
embedSamples,SingleCellExperiment-method	embedSamples
enrichment.test	enrichment.test
exSCE	exSCE
featureNames,SingleCellExperiment-method	featureNames-SingleCellExperiment-method
filterTrajFeaturesByCOV	filterTrajFeaturesByCOV
filterTrajFeaturesByCOV,SingleCellExperiment-method	filterTrajFeaturesByCOV
filterTrajFeaturesByDL	filterTrajFeaturesByDL
filterTrajFeaturesByDL,SingleCellExperiment-method	filterTrajFeaturesByDL
filterTrajFeaturesByFF	filterTrajFeaturesByFF
filterTrajFeaturesByFF,SingleCellExperiment-method	filterTrajFeaturesByFF
findSpectrum	findSpectrum
findSpectrum,numeric-method	findSpectrum
findStates	findStates
findStates,SingleCellExperiment-method	findStates
fitDynamic	fitDynamic
fitDynamic,SingleCellExperiment-method	fitDynamic
fitTrajectory	fitTrajectory
fitTrajectory,SingleCellExperiment-method	fitTrajectory
landmarks	landmarks
landmarks,SingleCellExperiment-method	landmarks
latentSpace	latentSpace
latentSpace,SingleCellExperiment-method	latentSpace
latentSpace<-	latentSpace-set
latentSpace<-,SingleCellExperiment-method	latentSpace-set
manifold2D	manifold2D
manifold2D,SingleCellExperiment-method	manifold2D
manifold2D<-	manifold2D-set
manifold2D<-,SingleCellExperiment-method	manifold2D-set
pca	pca
pca,SingleCellExperiment-method	pca
phenoNames	phenoNames
phenoNames,SingleCellExperiment-method	phenoNames
plotDynamic	plotDynamic
plotDynamic,SingleCellExperiment-method	plotDynamic
plotManifold	plotManifold
plotManifold,SingleCellExperiment-method	plotManifold
plotMap	plotMap
plotMap,SingleCellExperiment-method	plotMap
plotStateExpression	plotStateExpression
plotStateExpression,SingleCellExperiment-method	plotStateExpression
plotStateSize	plotStateSize
plotStateSize,SingleCellExperiment-method	plotStateSize
plotStateTrajectory	plotStateTrajectory
plotStateTrajectory,SingleCellExperiment-method	plotStateTrajectory
plotTrail	plotTrail
plotTrail,SingleCellExperiment-method	plotTrail
plotTrajectoryFit	plotTrajectoryFit
plotTrajectoryFit,SingleCellExperiment-method	plotTrajectoryFit
read.ygraphml	read.ygraphml
removeTrail	removeTrail
removeTrail,SingleCellExperiment-method	removeTrail
sampleNames,SingleCellExperiment-method	sampleNames-SingleCellExperiment-method
selectTrajectory	selectTrajectory
selectTrajectory,SingleCellExperiment-method	selectTrajectory
showTrajInfo	showTrajInfo
showTrajInfo,SingleCellExperiment-method	showTrajInfo
simulate_exprs	simulate_exprs
states	states
states,SingleCellExperiment-method	states
states<-	states-set
states<-,SingleCellExperiment-method	states-set
stateTrajLayout<-	stateTrajLayout-set
stateTrajLayout<-,SingleCellExperiment-method	stateTrajLayout-set
trailNames	trailNames
trailNames,SingleCellExperiment-method	trailNames
trailNames<-	trailNames-set
trailNames<-,SingleCellExperiment-method	trailNames-set
trails	trails
trails,SingleCellExperiment-method	trails
trajComponents	trajComponents
trajComponents,SingleCellExperiment-method	trajComponents
trajFeatureNames	trajFeatureNames
trajFeatureNames,SingleCellExperiment-method	trajFeatureNames
trajFeatureNames<-	trajFeatureNames-set
trajFeatureNames<-,SingleCellExperiment-method	trajFeatureNames-set
trajLayout	trajLayout
trajLayout,SingleCellExperiment-method	trajLayout
trajLayout<-	trajLayout-set
trajLayout<-,SingleCellExperiment-method	trajLayout-set
trajResiduals	trajResiduals
trajResiduals,SingleCellExperiment-method	trajResiduals
trajSampleNames	trajSampleNames
trajSampleNames,SingleCellExperiment-method	trajSampleNames
userLandmarks	userLandmarks
userLandmarks,SingleCellExperiment-method	userLandmarks
userLandmarks<-	userLandmarks-set
userLandmarks<-,SingleCellExperiment-method	userLandmarks-set
write.ygraphml	write.ygraphml
write.ygraphml,SingleCellExperiment-method	write.ygraphml
