Reconstruction, visualization and analysis of branching trajectories


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Documentation for package ‘CellTrails’ version 1.20.0

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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