Files in elldc/CellTrails

Reconstruction, visualization and analysis of branching trajectories

R/AllClasses.R R/AllGenerics.R R/accessor-methods.R R/cluster-methods.R R/data-sets.R R/diffexp-methods.R R/dimred-methods.R R/export-methods.R R/filter-methods.R R/fitting-methods.R R/import-methods.R R/imputation-methods.R R/layout-methods.R R/plot-methods.R R/show-methods.R R/simulation-methods.R R/test-methods.R R/trajectory-methods.R R/utility-methods.R README.md docs/index.Rmd inst/scripts/make-data.R inst/unitTests/test_addTrail.R inst/unitTests/test_connectStates.R inst/unitTests/test_embedSamples.R inst/unitTests/test_findSpectrum.R inst/unitTests/test_findStates.R inst/unitTests/test_fitDynamic.R inst/unitTests/test_fitTrajectory.R inst/unitTests/test_phenoNames.R inst/unitTests/test_plotDynamic.R inst/unitTests/test_plotManifold.R inst/unitTests/test_plotMap.R inst/unitTests/test_plotStateExpression.R inst/unitTests/test_plotStateSize.R inst/unitTests/test_plotStateTrajectory.R inst/unitTests/test_plotTrail.R inst/unitTests/test_plotTrajectoryFit.R inst/unitTests/test_userLandmarks.R inst/unitTests/test_workflow_logic.R man/addTrail.Rd man/connectStates.Rd man/contrastTrailExpr.Rd man/dot-adjustLayoutByPtime.Rd man/dot-bhtsne.Rd man/dot-capitalize.Rd man/dot-color_hue.Rd man/dot-color_ramp.Rd man/dot-connectStates_def.Rd man/dot-connect_ordi.Rd man/dot-connect_ortho.Rd man/dot-contrastExprTrail_def.Rd man/dot-deleteMedianCentres.Rd man/dot-denoiseExpression.Rd man/dot-diffExpr.Rd man/dot-diffExprState_def.Rd man/dot-embedSamples_def.Rd man/dot-exprs.Rd man/dot-featureNameExists.Rd man/dot-filterTrajFeaturesByCOV_def.Rd man/dot-filterTrajFeaturesByDL_def.Rd man/dot-filterTrajFeaturesByFF_def.Rd man/dot-findSpectrum_def.Rd man/dot-findStates_def.Rd man/dot-fitDynamic_def.Rd man/dot-fitTrajectory_def.Rd man/dot-fit_surface.Rd man/dot-fr_layout.Rd man/dot-generate_ordination.Rd man/dot-ihs.Rd man/dot-linear_fit.Rd man/dot-needsToBeExpanded.Rd man/dot-nn_impute.Rd man/dot-pca_def.Rd man/dot-pheno.Rd man/dot-phenoNameExists.Rd man/dot-plotDynamic.Rd man/dot-plotManifold_def.Rd man/dot-plotSpectrum_def.Rd man/dot-plotStateExpression_def.Rd man/dot-plotStateSize_def.Rd man/dot-plotStateTrajectory_def.Rd man/dot-plotTrail_def.Rd man/dot-plotTrailblazing_def.Rd man/dot-plot_trajectoryFit.Rd man/dot-prettyColorRamp.Rd man/dot-prettyString.Rd man/dot-project_ortho.Rd man/dot-rbf.Rd man/dot-rescale.Rd man/dot-sampleNameExists.Rd man/dot-spanForest-set.Rd man/dot-spanForest.Rd man/dot-spatmed.Rd man/dot-stateTrajLayout.Rd man/dot-trailNameExists.Rd man/dot-trajGraph-set.Rd man/dot-trajGraph.Rd man/dot-trajLandmark-set.Rd man/dot-trajLandmark.Rd man/dot-trajResiduals-set.Rd man/dot-useFeature-set.Rd man/dot-useFeature.Rd man/dot-useSample-set.Rd man/dot-useSample.Rd man/dot-validatePlotParams.Rd man/dot-write_ygraphml_def.Rd man/embedSamples.Rd man/enrichment.test.Rd man/exSCE.Rd man/featureNames-SingleCellExperiment-method.Rd man/filterTrajFeaturesByCOV.Rd man/filterTrajFeaturesByDL.Rd man/filterTrajFeaturesByFF.Rd man/findSpectrum.Rd man/findStates.Rd man/fitDynamic.Rd man/fitTrajectory.Rd man/landmarks.Rd man/latentSpace-set.Rd man/latentSpace.Rd man/manifold2D-set.Rd man/manifold2D.Rd man/pca.Rd man/phenoNames.Rd man/plotDynamic.Rd man/plotManifold.Rd man/plotMap.Rd man/plotStateExpression.Rd man/plotStateSize.Rd man/plotStateTrajectory.Rd man/plotTrail.Rd man/plotTrajectoryFit.Rd man/read.ygraphml.Rd man/removeTrail.Rd man/sampleNames-SingleCellExperiment-method.Rd man/selectTrajectory.Rd man/showTrajInfo.Rd man/simulate_exprs.Rd man/stateTrajLayout-set.Rd man/states-set.Rd man/states.Rd man/trailNames-set.Rd man/trailNames.Rd man/trails.Rd man/trajComponents.Rd man/trajFeatureNames-set.Rd man/trajFeatureNames.Rd man/trajLayout-set.Rd man/trajLayout.Rd man/trajResiduals.Rd man/trajSampleNames.Rd man/userLandmarks-set.Rd man/userLandmarks.Rd man/write.ygraphml.Rd tests/runTests.R vignettes/vignette.Rmd