Package: TrajectoryUtils 1.13.0

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_1.13.0.tar.gz
TrajectoryUtils_1.13.0.zip(r-4.5)TrajectoryUtils_1.13.0.zip(r-4.4)TrajectoryUtils_1.13.0.zip(r-4.3)
TrajectoryUtils_1.13.0.tgz(r-4.4-any)TrajectoryUtils_1.13.0.tgz(r-4.3-any)
TrajectoryUtils_1.13.0.tar.gz(r-4.5-noble)TrajectoryUtils_1.13.0.tar.gz(r-4.4-noble)
TrajectoryUtils_1.13.0.tgz(r-4.4-emscripten)TrajectoryUtils_1.13.0.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-1.13.0(bioc 3.20)TrajectoryUtils-1.12.0(bioc 3.19)

bioconductor-package

25 exports 2.35 score 38 dependencies 9 dependents

Last updated 2 months agofrom:01b5a90a53

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 askpass Biobase BiocGenerics cli cpp11 crayon curl DelayedArray GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr igraph IRanges jsonlite lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pkgconfig R6 rlang S4Arrays S4Vectors SingleCellExperiment SparseArray SummarizedExperiment sys UCSC.utils vctrs XVector zlibbioc

Trajectory utilities for package developers

Aaron Lun

Rendered fromoverview.Rmdusingknitr::rmarkdownon Jun 17 2024.

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