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:Aaron Lun [aut, cre], Kelly Street [aut]

TrajectoryUtils_1.15.0.tar.gz
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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'))

Peer review:

Bug tracker:https://github.com/ltla/trajectoryutils/issues

On BioConductor:TrajectoryUtils-1.15.0(bioc 3.21)TrajectoryUtils-1.14.0(bioc 3.20)

geneexpressionsinglecell

6.04 score 9 packages 15 scripts 3.0k downloads 25 exports 39 dependencies

Last updated 23 days agofrom:80a5e71a90. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macWARNINGNov 18 2024
R-4.3-winWARNINGNov 18 2024
R-4.3-macWARNINGNov 18 2024

Exports:averagePseudotimecellDatacellData<-cellnamescellnames<-createClusterMSTdefineMSTPathsguessMSTRootsncellsnpathspathDatapathData<-pathnamespathnames<-pathStatpathStat<-pathStatNamespathStatNames<-pathStatspathStats<-PseudotimeOrderingrowmeanrowmedianshowsplitByBranches

Dependencies:abindaskpassBiobaseBiocGenericsclicpp11crayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrigraphIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpkgconfigR6rlangS4ArraysS4VectorsSingleCellExperimentSparseArraySummarizedExperimentsysUCSC.utilsvctrsXVectorzlibbioc

Trajectory utilities for package developers

Aaron Lun

Rendered fromoverview.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2020-11-30
Started: 2020-11-09

Readme and manuals

Help Manual

Help pageTopics
Compute the average pseudotimeaveragePseudotime
Minimum spanning trees on cluster centroidscreateClusterMST createClusterMST,ANY-method createClusterMST,SingleCellExperiment-method createClusterMST,SummarizedExperiment-method
Define paths through the MSTdefineMSTPaths
Guess the roots of a MSTguessMSTRoots
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 variablerowmean rowmedian
Split a graph into branch-free pathssplitByBranches