Package: TrajectoryUtils 1.15.0
Aaron Lun
TrajectoryUtils: Single-Cell Trajectory Analysis Utilities
Implements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. Include a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime inference results.
Authors:
TrajectoryUtils_1.15.0.tar.gz
TrajectoryUtils_1.15.0.zip(r-4.5)TrajectoryUtils_1.15.0.zip(r-4.4)TrajectoryUtils_1.15.0.zip(r-4.3)
TrajectoryUtils_1.15.0.tgz(r-4.4-any)TrajectoryUtils_1.15.0.tgz(r-4.3-any)
TrajectoryUtils_1.15.0.tar.gz(r-4.5-noble)TrajectoryUtils_1.15.0.tar.gz(r-4.4-noble)
TrajectoryUtils_1.15.0.tgz(r-4.4-emscripten)TrajectoryUtils_1.15.0.tgz(r-4.3-emscripten)
TrajectoryUtils.pdf |TrajectoryUtils.html✨
TrajectoryUtils/json (API)
| # Install 'TrajectoryUtils' in R: |
| install.packages('TrajectoryUtils', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ltla/trajectoryutils/issues
On BioConductor:TrajectoryUtils-1.15.0(bioc 3.21)TrajectoryUtils-1.14.0(bioc 3.20)
Last updated 2 months agofrom:80a5e71a90. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win | NOTE | Dec 18 2024 |
| R-4.5-linux | NOTE | Dec 18 2024 |
| R-4.4-win | OK | Dec 18 2024 |
| R-4.4-mac | OK | Dec 18 2024 |
| R-4.3-win | OK | Dec 18 2024 |
| R-4.3-mac | OK | Dec 18 2024 |
Exports:averagePseudotimecellDatacellData<-cellnamescellnames<-createClusterMSTdefineMSTPathsguessMSTRootsncellsnpathspathDatapathData<-pathnamespathnames<-pathStatpathStat<-pathStatNamespathStatNames<-pathStatspathStats<-PseudotimeOrderingrowmeanrowmedianshowsplitByBranches
Dependencies:abindaskpassBiobaseBiocGenericsclicpp11crayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrigraphIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpkgconfigR6rlangS4ArraysS4VectorsSingleCellExperimentSparseArraySummarizedExperimentsysUCSC.utilsvctrsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute the average pseudotime | averagePseudotime |
| Minimum spanning trees on cluster centroids | createClusterMST createClusterMST,ANY-method createClusterMST,SingleCellExperiment-method createClusterMST,SummarizedExperiment-method |
| Define paths through the MST | defineMSTPaths |
| Guess the roots of a MST | guessMSTRoots |
| The PseudotimeOrdering class | $,PseudotimeOrdering-method $<-,PseudotimeOrdering-method cellData cellData<- cellData<-,PseudotimeOrdering-method cellnames cellnames<- cellnames<-,PseudotimeOrdering-method ncells npaths pathData pathData<- pathData<-,PseudotimeOrdering-method pathnames pathnames<- pathnames<-,PseudotimeOrdering-method pathStat pathStat<- pathStat<-,PseudotimeOrdering-method pathStatNames pathStatNames<- pathStatNames<-,PseudotimeOrdering-method pathStats pathStats<- pathStats<-,PseudotimeOrdering-method PseudotimeOrdering PseudotimeOrdering-class show,PseudotimeOrdering-method |
| Compute column means based on a grouping variable | rowmean rowmedian |
| Split a graph into branch-free paths | splitByBranches |
