Reconstruction, visualization and analysis of branching
trajectories
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Documentation for package ‘CellTrails’ version 1.20.0
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 |