Package: CellTrails 1.25.0
Daniel Ellwanger
CellTrails: Reconstruction, visualization and analysis of branching trajectories
CellTrails is an unsupervised algorithm for the de novo chronological ordering, visualization and analysis of single-cell expression data. CellTrails makes use of a geometrically motivated concept of lower-dimensional manifold learning, which exhibits a multitude of virtues that counteract intrinsic noise of single cell data caused by drop-outs, technical variance, and redundancy of predictive variables. CellTrails enables the reconstruction of branching trajectories and provides an intuitive graphical representation of expression patterns along all branches simultaneously. It allows the user to define and infer the expression dynamics of individual and multiple pathways towards distinct phenotypes.
Authors:
CellTrails_1.25.0.tar.gz
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CellTrails_1.25.0.tgz(r-4.4-any)CellTrails_1.25.0.tgz(r-4.3-any)
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CellTrails.pdf |CellTrails.html✨
CellTrails/json (API)
NEWS
| # Install 'CellTrails' in R: |
| install.packages('CellTrails', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- exSCE - Example single-cell expression data
On BioConductor:CellTrails-1.25.0(bioc 3.21)CellTrails-1.24.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyclusteringdatarepresentationdifferentialexpressiondimensionreductiongeneexpressionsequencingsinglecellsoftwaretimecourse
Last updated 2 months agofrom:b064f5012f. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Nov 29 2024 |
Exports:addTrailconnectStatescontrastTrailExprembedSamplesenrichment.testfeatureNamesfilterTrajFeaturesByCOVfilterTrajFeaturesByDLfilterTrajFeaturesByFFfindSpectrumfindStatesfitDynamicfitTrajectorylandmarkslatentSpacelatentSpace<-manifold2Dmanifold2D<-pcaphenoNamesplotDynamicplotManifoldplotMapplotStateExpressionplotStateSizeplotStateTrajectoryplotTrailplotTrajectoryFitread.ygraphmlremoveTrailsampleNamesselectTrajectoryshowTrajInfosimulate_exprsstatesstates<-stateTrajLayout<-trailNamestrailNames<-trailstrajComponentstrajFeatureNamestrajFeatureNames<-trajLayouttrajLayout<-trajResidualstrajSampleNamesuserLandmarksuserLandmarks<-write.ygraphml
Dependencies:abindaskpassBiobaseBiocGenericscbacliclustercolorspacecpp11crayoncurlDelayedArraydendextenddtwEnvStatsfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegridExtragtablehttrigraphIRangesisobandjsonlitelabelinglatticelifecyclemagrittrmaptreeMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmenortestopensslpillarpkgconfigplyrproxyR6RColorBrewerRcppreshape2rlangrpartRtsneS4ArraysS4VectorsscalesSingleCellExperimentSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ADD trail | addTrail addTrail,SingleCellExperiment-method |
| Connect trajectory states | connectStates connectStates,SingleCellExperiment-method |
| Differential trail expression analysis | contrastTrailExpr contrastTrailExpr,SingleCellExperiment-method |
| Spectral embedding of biological samples | embedSamples embedSamples,matrix-method embedSamples,SingleCellExperiment-method |
| Enrichment test | enrichment.test |
| Example single-cell expression data | exSCE |
| GET feature names | featureNames,SingleCellExperiment-method |
| Filter features by Coefficient of Variation (COV) | filterTrajFeaturesByCOV filterTrajFeaturesByCOV,SingleCellExperiment-method |
| Filter trajectory features by Detection Level (DL) | filterTrajFeaturesByDL filterTrajFeaturesByDL,SingleCellExperiment-method |
| Filter features by Fano Factor | filterTrajFeaturesByFF filterTrajFeaturesByFF,SingleCellExperiment-method |
| Determine number of informative latent dimensions | findSpectrum findSpectrum,numeric-method |
| Identify trajectory states | findStates findStates,SingleCellExperiment-method |
| Fit expression dynamic | fitDynamic fitDynamic,SingleCellExperiment-method |
| Align samples to trajectory | fitTrajectory fitTrajectory,SingleCellExperiment-method |
| GET landmarks | landmarks landmarks,SingleCellExperiment-method |
| GET CellTrails' latent space | latentSpace latentSpace,SingleCellExperiment-method |
| SET latent space | latentSpace<- latentSpace<-,SingleCellExperiment-method |
| GET 2D manifold representation | manifold2D manifold2D,SingleCellExperiment-method |
| SET 2D manifold representation | manifold2D<- manifold2D<-,SingleCellExperiment-method |
| Principal Component Analysis | pca pca,SingleCellExperiment-method |
| GET phenotype names | phenoNames phenoNames,SingleCellExperiment-method |
| Visualize dynamics | plotDynamic plotDynamic,SingleCellExperiment-method |
| Visualize the learned manifold | plotManifold plotManifold,SingleCellExperiment-method |
| Visualize expression maps | plotMap plotMap,SingleCellExperiment-method |
| Visualize feature expression distribution per state | plotStateExpression plotStateExpression,SingleCellExperiment-method |
| Visualize the number of samples per state | plotStateSize plotStateSize,SingleCellExperiment-method |
| Visualize state trajectory graph | plotStateTrajectory plotStateTrajectory,SingleCellExperiment-method |
| Visualize single trails | plotTrail plotTrail,SingleCellExperiment-method |
| Visualize trajectory fit residuals | plotTrajectoryFit plotTrajectoryFit,SingleCellExperiment-method |
| Reads trajectory graph layout | read.ygraphml |
| REMOVE trail | removeTrail removeTrail,SingleCellExperiment-method |
| GET sample names | sampleNames,SingleCellExperiment-method |
| Select component from trajectory graph | selectTrajectory selectTrajectory,SingleCellExperiment-method |
| Shows relevant content of a SingleCellExperiment object for a CellTrails analysis | showTrajInfo showTrajInfo,SingleCellExperiment-method |
| Simulation of RNA-Seq expression data | simulate_exprs |
| GET states | states states,SingleCellExperiment-method |
| SET states | states<- states<-,SingleCellExperiment-method |
| SET state trajectory layout | stateTrajLayout<- stateTrajLayout<-,SingleCellExperiment-method |
| GET trail names | trailNames trailNames,SingleCellExperiment-method |
| SET trail names | trailNames<- trailNames<-,SingleCellExperiment-method |
| GET trails | trails trails,SingleCellExperiment-method |
| GET trajectory component states | trajComponents trajComponents,SingleCellExperiment-method |
| GET trajectory feature names | trajFeatureNames trajFeatureNames,SingleCellExperiment-method |
| SET trajectory features by name | trajFeatureNames<- trajFeatureNames<-,SingleCellExperiment-method |
| GET trajectory layout | trajLayout trajLayout,SingleCellExperiment-method |
| SET trajectory layout | trajLayout<- trajLayout<-,SingleCellExperiment-method |
| GET trajectory fitting residuals | trajResiduals trajResiduals,SingleCellExperiment-method |
| GET trajectory sample names | trajSampleNames trajSampleNames,SingleCellExperiment-method |
| GET user-defined landmarks | userLandmarks userLandmarks,SingleCellExperiment-method |
| SET user-defined landmarks | userLandmarks<- userLandmarks<-,SingleCellExperiment-method |
| Export trajectory graph | write.ygraphml write.ygraphml,SingleCellExperiment-method |
