Package: TrajectoryUtils 1.20.0

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_1.20.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
TrajectoryUtils/json (API)

# Install 'TrajectoryUtils' in R:
install.packages('TrajectoryUtils', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

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

On BioConductor:TrajectoryUtils-1.21.0(bioc 3.24)TrajectoryUtils-1.20.0(bioc 3.23)

geneexpressionsinglecell

6.01 score 8 packages 18 scripts 3.9k downloads 25 exports 27 dependencies

Last updated from:72c185ebc0 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING196
linux-devel-x86_64NOTE333
source / vignettesOK232
linux-release-x86_64NOTE289
macos-release-arm64NOTE248
macos-oldrel-arm64NOTE223
windows-develNOTE589
windows-releaseNOTE521
windows-oldrelNOTE508
wasm-releaseOK135

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

Dependencies:abindBiobaseBiocGenericsclicpp11DelayedArraygenericsGenomicRangesglueigraphIRangeslatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatspkgconfigrlangS4ArraysS4VectorsSeqinfoSingleCellExperimentSparseArraySummarizedExperimentvctrsXVector

Trajectory utilities for package developers

Aaron Lun

Rendered fromoverview.Rmdusingknitr::rmarkdownon May 29 2026.

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