.adjustLayoutByPtime	dot-adjustLayoutByPtime
.bhtsne	dot-bhtsne
.capitalize	dot-capitalize
.color_hue	dot-color_hue
.color_ramp	dot-color_ramp
.connectStates_def	dot-connectStates_def
.connect_ordi	dot-connect_ordi
.connect_ortho	dot-connect_ortho
.contrastExprTrail_def	dot-contrastExprTrail_def
.deleteMedianCentres	dot-deleteMedianCentres
.denoiseExpression	dot-denoiseExpression
.diffExpr	dot-diffExpr
.diffExprState_def	dot-diffExprState_def
.embedSamples_def	dot-embedSamples_def
.exprs	dot-exprs
.exprs,SingleCellExperiment-method	dot-exprs
.featureNameExists	dot-featureNameExists
.filterTrajFeaturesByCOV_def	dot-filterTrajFeaturesByCOV_def
.filterTrajFeaturesByDL_def	dot-filterTrajFeaturesByDL_def
.filterTrajFeaturesByFF_def	dot-filterTrajFeaturesByFF_def
.findSpectrum_def	dot-findSpectrum_def
.findStates_def	dot-findStates_def
.fitDynamic_def	dot-fitDynamic_def
.fitTrajectory_def	dot-fitTrajectory_def
.fit_surface	dot-fit_surface
.fr_layout	dot-fr_layout
.generate_ordination	dot-generate_ordination
.ihs	dot-ihs
.linear_fit	dot-linear_fit
.needsToBeExpanded	dot-needsToBeExpanded
.nn_impute	dot-nn_impute
.pca_def	dot-pca_def
.pheno	dot-pheno
.pheno,SingleCellExperiment-method	dot-pheno
.phenoNameExists	dot-phenoNameExists
.plotDynamic	dot-plotDynamic
.plotManifold_def	dot-plotManifold_def
.plotSpectrum_def	dot-plotSpectrum_def
.plotStateExpression_def	dot-plotStateExpression_def
.plotStateSize_def	dot-plotStateSize_def
.plotStateTrajectory_def	dot-plotStateTrajectory_def
.plotTrailblazing_def	dot-plotTrailblazing_def
.plotTrail_def	dot-plotTrail_def
.plot_trajectoryFit	dot-plot_trajectoryFit
.prettyColorRamp	dot-prettyColorRamp
.prettyString	dot-prettyString
.project_ortho	dot-project_ortho
.rbf	dot-rbf
.rescale	dot-rescale
.sampleNameExists	dot-sampleNameExists
.spanForest	dot-spanForest
.spanForest,SingleCellExperiment-method	dot-spanForest
.spanForest<-	dot-spanForest-set
.spanForest<-,SingleCellExperiment-method	dot-spanForest-set
.spatmed	dot-spatmed
.stateTrajLayout	dot-stateTrajLayout
.stateTrajLayout,SingleCellExperiment-method	dot-stateTrajLayout
.trailNameExists	dot-trailNameExists
.trajGraph	dot-trajGraph
.trajGraph,SingleCellExperiment-method	dot-trajGraph
.trajGraph<-	dot-trajGraph-set
.trajGraph<-,SingleCellExperiment-method	dot-trajGraph-set
.trajLandmark	dot-trajLandmark
.trajLandmark,SingleCellExperiment-method	dot-trajLandmark
.trajLandmark<-	dot-trajLandmark-set
.trajLandmark<-,SingleCellExperiment-method	dot-trajLandmark-set
.trajResiduals<-	dot-trajResiduals-set
.trajResiduals<-,SingleCellExperiment-method	dot-trajResiduals-set
.useFeature	dot-useFeature
.useFeature,SingleCellExperiment-method	dot-useFeature
.useFeature<-	dot-useFeature-set
.useFeature<-,SingleCellExperiment-method	dot-useFeature-set
.useSample	dot-useSample
.useSample,SingleCellExperiment-method	dot-useSample
.useSample<-	dot-useSample-set
.validatePlotParams	dot-validatePlotParams
.write_ygraphml_def	dot-write_ygraphml_def
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
useSample<-,SingleCellExperiment-method	dot-useSample-set
write.ygraphml	write.ygraphml
write.ygraphml,SingleCellExperiment-method	write.ygraphml
