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 |