API for elldc/CellTrails
Reconstruction, visualization and analysis of branching trajectories

Global functions
addTrail Man page
addTrail,SingleCellExperiment-method Man page
adjustLayoutByPtime Source code
bhtsne Source code
capitalize Source code
color_hue Source code
color_ramp Source code
connectStates Man page
connectStates,SingleCellExperiment-method Man page
connectStates_def Source code
connect_ordi Source code
connect_ortho Source code
contrastExprTrail_def Source code
contrastTrailExpr Man page
contrastTrailExpr,SingleCellExperiment-method Man page
deleteMedianCentres Source code
denoiseExpression Source code
diffExpr Source code
diffExprState_def Source code
embedSamples Man page
embedSamples,SingleCellExperiment-method Man page
embedSamples,matrix-method Man page
embedSamples_def Source code
enrichment.test Man page Source code
exSCE Man page
featureNameExists Source code
featureNames,SingleCellExperiment-method Man page
filterTrajFeaturesByCOV Man page
filterTrajFeaturesByCOV,SingleCellExperiment-method Man page
filterTrajFeaturesByCOV_def Source code
filterTrajFeaturesByDL Man page
filterTrajFeaturesByDL,SingleCellExperiment-method Man page
filterTrajFeaturesByDL_def Source code
filterTrajFeaturesByFF Man page
filterTrajFeaturesByFF,SingleCellExperiment-method Man page
filterTrajFeaturesByFF_def Source code
findSpectrum Man page
findSpectrum,numeric-method Man page
findSpectrum_def Source code
findStates Man page
findStates,SingleCellExperiment-method Man page
findStates_def Source code
fitDynamic Man page
fitDynamic,SingleCellExperiment-method Man page
fitDynamic_def Source code
fitTrajectory Man page
fitTrajectory,SingleCellExperiment-method Man page
fitTrajectory_def Source code
fit_surface Source code
fr_layout Source code
generate_ordination Source code
hs Source code
landmarks Man page
landmarks,SingleCellExperiment-method Man page
latentSpace Man page
latentSpace,SingleCellExperiment-method Man page
latentSpace<- Man page
latentSpace<-,SingleCellExperiment-method Man page
linear_fit Source code
manifold2D Man page
manifold2D,SingleCellExperiment-method Man page
manifold2D<- Man page
manifold2D<-,SingleCellExperiment-method Man page
needsToBeExpanded Source code
nn_impute Source code
pca Man page
pca,SingleCellExperiment-method Man page
pca_def Source code
phenoNameExists Source code
phenoNames Man page
phenoNames,SingleCellExperiment-method Man page
plotDynamic Man page Source code
plotDynamic,SingleCellExperiment-method Man page
plotManifold Man page
plotManifold,SingleCellExperiment-method Man page
plotManifold_def Source code
plotMap Man page
plotMap,SingleCellExperiment-method Man page
plotSpectrum_def Source code
plotStateExpression Man page
plotStateExpression,SingleCellExperiment-method Man page
plotStateExpression_def Source code
plotStateSize Man page
plotStateSize,SingleCellExperiment-method Man page
plotStateSize_def Source code
plotStateTrajectory Man page
plotStateTrajectory,SingleCellExperiment-method Man page
plotStateTrajectory_def Source code
plotTrail Man page
plotTrail,SingleCellExperiment-method Man page
plotTrail_def Source code
plotTrailblazing_def Source code
plotTrajectoryFit Man page
plotTrajectoryFit,SingleCellExperiment-method Man page
plot_trajectoryFit Source code
prettyColorRamp Source code
prettyString Source code
project_ortho Source code
rbf Source code
read.ygraphml Man page Source code
removeTrail Man page
removeTrail,SingleCellExperiment-method Man page
rescale Source code
sampleNameExists Source code
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
spatmed 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
trailNameExists Source code
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
validatePlotParams Source code
write.ygraphml Man page
write.ygraphml,SingleCellExperiment-method Man page
write_ygraphml_def Source code
elldc/CellTrails documentation built on Aug. 16, 2018, 3:50 a.m.