addTrail                ADD trail
connectStates           Connect trajectory states
contrastTrailExpr       Differential trail expression analysis
embedSamples            Spectral embedding of biological samples
enrichment.test         Enrichment test
exSCE                   Example single-cell expression data
featureNames,SingleCellExperiment-method
                        GET feature names
filterTrajFeaturesByCOV
                        Filter features by Coefficient of Variation
                        (COV)
filterTrajFeaturesByDL
                        Filter trajectory features by Detection Level
                        (DL)
filterTrajFeaturesByFF
                        Filter features by Fano Factor
findSpectrum            Determine number of informative latent
                        dimensions
findStates              Identify trajectory states
fitDynamic              Fit expression dynamic
fitTrajectory           Align samples to trajectory
landmarks               GET landmarks
latentSpace             GET CellTrails' latent space
latentSpace<-           SET latent space
manifold2D              GET 2D manifold representation
manifold2D<-            SET 2D manifold representation
pca                     Principal Component Analysis
phenoNames              GET phenotype names
plotDynamic             Visualize dynamics
plotManifold            Visualize the learned manifold
plotMap                 Visualize expression maps
plotStateExpression     Visualize feature expression distribution per
                        state
plotStateSize           Visualize the number of samples per state
plotStateTrajectory     Visualize state trajectory graph
plotTrail               Visualize single trails
plotTrajectoryFit       Visualize trajectory fit residuals
read.ygraphml           Reads trajectory graph layout
removeTrail             REMOVE trail
sampleNames,SingleCellExperiment-method
                        GET sample names
selectTrajectory        Select component from trajectory graph
showTrajInfo            Shows relevant content of a
                        SingleCellExperiment object for a CellTrails
                        analysis
simulate_exprs          Simulation of RNA-Seq expression data
stateTrajLayout<-       SET state trajectory layout
states                  GET states
states<-                SET states
trailNames              GET trail names
trailNames<-            SET trail names
trails                  GET trails
trajComponents          GET trajectory component states
trajFeatureNames        GET trajectory feature names
trajFeatureNames<-      SET trajectory features by name
trajLayout              GET trajectory layout
trajLayout<-            SET trajectory layout
trajResiduals           GET trajectory fitting residuals
trajSampleNames         GET trajectory sample names
userLandmarks           GET user-defined landmarks
userLandmarks<-         SET user-defined landmarks
write.ygraphml          Export trajectory graph
