Package: TrajectoryUtils 1.21.0

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]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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-1.21.0(bioc 3.24)TrajectoryUtils-1.20.0(bioc 3.23)

geneexpression singlecell

6.08 score 1 stars 8 packages 21 scripts 3.9k downloads 25 exports 27 dependencies

Last updated from:79012de5a3. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	175
linux-devel-x86_64	NOTE	292
source / vignettes	OK	250
linux-release-x86_64	NOTE	297
macos-release-arm64	NOTE	215
macos-oldrel-arm64	NOTE	169
windows-devel	NOTE	198
windows-release	NOTE	208
windows-oldrel	NOTE	208
wasm-release	OK	138

Exports:averagePseudotime cellData cellData<-cellnames cellnames<-createClusterMST defineMSTPaths guessMSTRoots ncells npaths pathData pathData<-pathnames pathnames<-pathStat pathStat<-pathStatNames pathStatNames<-pathStats pathStats<-PseudotimeOrdering rowmean rowmedian show splitByBranches

Dependencies:abind Biobase BiocGenerics cli cpp11 DelayedArray generics GenomicRanges glue igraph IRanges lattice lifecycle magrittr Matrix MatrixGenerics matrixStats pkgconfig rlang S4Arrays S4Vectors Seqinfo SingleCellExperiment SparseArray SummarizedExperiment vctrs XVector

Trajectory utilities for package developers

Overview | MST construction | Operations on the MST | The PseudotimeOrdering class | Session information

Rendered fromoverview.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

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