# Reconstruction, visualization and analysis of branching trajectories

## Documentation for package ‘CellTrails’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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