API for CellTrails
Reconstruction, visualization and analysis of branching trajectories

Global functions
.adjustLayoutByPtime Source code
.bhtsne Source code
.capitalize Source code
.color_hue Source code
.color_ramp Source code
.connectStates_def Source code
.connect_ordi Source code
.connect_ortho Source code
.contrastExprTrail_def Source code
.deleteMedianCentres Source code
.denoiseExpression Source code
.diffExpr Source code
.diffExprState_def Source code
.embedSamples_def Source code
.featureNameExists Source code
.filterTrajFeaturesByCOV_def Source code
.filterTrajFeaturesByDL_def Source code
.filterTrajFeaturesByFF_def Source code
.findSpectrum_def Source code
.findStates_def Source code
.fitDynamic_def Source code
.fitTrajectory_def Source code
.fit_surface Source code
.fr_layout Source code
.generate_ordination Source code
.ihs Source code
.linear_fit Source code
.needsToBeExpanded Source code
.nn_impute Source code
.pca_def Source code
.phenoNameExists Source code
.plotDynamic Source code
.plotManifold_def Source code
.plotSpectrum_def Source code
.plotStateExpression_def Source code
.plotStateSize_def Source code
.plotStateTrajectory_def Source code
.plotTrail_def Source code
.plotTrailblazing_def Source code
.plot_trajectoryFit Source code
.prettyColorRamp Source code
.prettyString Source code
.project_ortho Source code
.rbf Source code
.rescale Source code
.sampleNameExists Source code
.trailNameExists Source code
.validatePlotParams Source code
.write_ygraphml_def Source code
addTrail Man page
addTrail,SingleCellExperiment-method Man page
connectStates Man page
connectStates,SingleCellExperiment-method Man page
contrastTrailExpr Man page
contrastTrailExpr,SingleCellExperiment-method Man page
embedSamples Man page
embedSamples,SingleCellExperiment-method Man page
embedSamples,matrix-method Man page
enrichment.test Man page Source code
exSCE Man page
featureNames,SingleCellExperiment-method Man page
filterTrajFeaturesByCOV Man page
filterTrajFeaturesByCOV,SingleCellExperiment-method Man page
filterTrajFeaturesByDL Man page
filterTrajFeaturesByDL,SingleCellExperiment-method Man page
filterTrajFeaturesByFF Man page
filterTrajFeaturesByFF,SingleCellExperiment-method Man page
findSpectrum Man page
findSpectrum,numeric-method Man page
findStates Man page
findStates,SingleCellExperiment-method Man page
fitDynamic Man page
fitDynamic,SingleCellExperiment-method Man page
fitTrajectory Man page
fitTrajectory,SingleCellExperiment-method Man page
landmarks Man page
landmarks,SingleCellExperiment-method Man page
latentSpace Man page
latentSpace,SingleCellExperiment-method Man page
latentSpace<- Man page
latentSpace<-,SingleCellExperiment-method Man page
manifold2D Man page
manifold2D,SingleCellExperiment-method Man page
manifold2D<- Man page
manifold2D<-,SingleCellExperiment-method Man page
pca Man page
pca,SingleCellExperiment-method Man page
phenoNames Man page
phenoNames,SingleCellExperiment-method Man page
plotDynamic Man page
plotDynamic,SingleCellExperiment-method Man page
plotManifold Man page
plotManifold,SingleCellExperiment-method Man page
plotMap Man page
plotMap,SingleCellExperiment-method Man page
plotStateExpression Man page
plotStateExpression,SingleCellExperiment-method Man page
plotStateSize Man page
plotStateSize,SingleCellExperiment-method Man page
plotStateTrajectory Man page
plotStateTrajectory,SingleCellExperiment-method Man page
plotTrail Man page
plotTrail,SingleCellExperiment-method Man page
plotTrajectoryFit Man page
plotTrajectoryFit,SingleCellExperiment-method Man page
read.ygraphml Man page Source code
removeTrail Man page
removeTrail,SingleCellExperiment-method Man page
sampleNames,SingleCellExperiment-method Man page
selectTrajectory Man page
selectTrajectory,SingleCellExperiment-method Man page
showTrajInfo Man page
showTrajInfo,SingleCellExperiment-method Man page
simulate_exprs Man page Source code
stateTrajLayout<- Man page
stateTrajLayout<-,SingleCellExperiment-method Man page
states Man page
states,SingleCellExperiment-method Man page
states<- Man page
states<-,SingleCellExperiment-method Man page
trailNames Man page
trailNames,SingleCellExperiment-method Man page
trailNames<- Man page
trailNames<-,SingleCellExperiment-method Man page
trails Man page
trails,SingleCellExperiment-method Man page
trajComponents Man page
trajComponents,SingleCellExperiment-method Man page
trajFeatureNames Man page
trajFeatureNames,SingleCellExperiment-method Man page
trajFeatureNames<- Man page
trajFeatureNames<-,SingleCellExperiment-method Man page
trajLayout Man page
trajLayout,SingleCellExperiment-method Man page
trajLayout<- Man page
trajLayout<-,SingleCellExperiment-method Man page
trajResiduals Man page
trajResiduals,SingleCellExperiment-method Man page
trajSampleNames Man page
trajSampleNames,SingleCellExperiment-method Man page
userLandmarks Man page
userLandmarks,SingleCellExperiment-method Man page
userLandmarks<- Man page
userLandmarks<-,SingleCellExperiment-method Man page
write.ygraphml Man page
write.ygraphml,SingleCellExperiment-method Man page
CellTrails documentation built on Oct. 31, 2019, 5:46 a.m.