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

addTrailADD trail
connectStatesConnect trajectory states
contrastTrailExprDifferential trail expression analysis
embedSamplesSpectral embedding of biological samples
enrichment.testEnrichment test
exSCEExample single-cell expression data
featureNames-SingleCellExperiment-methodGET feature names
filterTrajFeaturesByCOVFilter features by Coefficient of Variation (COV)
filterTrajFeaturesByDLFilter trajectory features by Detection Level (DL)
filterTrajFeaturesByFFFilter features by Fano Factor
findSpectrumDetermine number of informative latent dimensions
findStatesIdentify trajectory states
fitDynamicFit expression dynamic
fitTrajectoryAlign samples to trajectory
landmarksGET landmarks
latentSpaceGET CellTrails' latent space
latentSpace-setSET latent space
manifold2DGET 2D manifold representation
manifold2D-setSET 2D manifold representation
pcaPrincipal Component Analysis
phenoNamesGET phenotype names
plotDynamicVisualize dynamics
plotManifoldVisualize the learned manifold
plotMapVisualize expression maps
plotStateExpressionVisualize feature expression distribution per state
plotStateSizeVisualize the number of samples per state
plotStateTrajectoryVisualize state trajectory graph
plotTrailVisualize single trails
plotTrajectoryFitVisualize trajectory fit residuals
read.ygraphmlReads trajectory graph layout
removeTrailREMOVE trail
sampleNames-SingleCellExperiment-methodGET sample names
selectTrajectorySelect component from trajectory graph
showTrajInfoShows relevant content of a SingleCellExperiment object for a...
simulate_exprsSimulation of RNA-Seq expression data
statesGET states
states-setSET states
stateTrajLayout-setSET state trajectory layout
trailNamesGET trail names
trailNames-setSET trail names
trailsGET trails
trajComponentsGET trajectory component states
trajFeatureNamesGET trajectory feature names
trajFeatureNames-setSET trajectory features by name
trajLayoutGET trajectory layout
trajLayout-setSET trajectory layout
trajResidualsGET trajectory fitting residuals
trajSampleNamesGET trajectory sample names
userLandmarksGET user-defined landmarks
userLandmarks-setSET user-defined landmarks
write.ygraphmlExport trajectory graph
elldc/CellTrails documentation built on Aug. 16, 2018, 3:50 a.m.