Files in elldc/CellTrails
Reconstruction, visualization and analysis of branching trajectories
.Rbuildignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
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
data/exSCE.rda
docs/index.Rmd
docs/index.html
inst/CITATION
inst/exdata/bundle.graphml
inst/exdata/bundle.rds
inst/exdata/exSCE.graphml
inst/exdata/th2.rds
inst/scripts/make-data.R
inst/unitTests/.Rapp.history
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
