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Single-Cell Trajectory Analysis Utilities

Bioconductor version: Release (3.19)

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.

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

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at>

Citation (from within R, enter citation("TrajectoryUtils")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Trajectory utilities HTML R Script
Reference Manual PDF


biocViews GeneExpression, SingleCell, Software
Version 1.12.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends SingleCellExperiment
Imports methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment
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Suggests BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown
Linking To
Depends On Me slingshot, TSCAN
Imports Me condiments, singleCellTK, tradeSeq
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package TrajectoryUtils_1.12.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) TrajectoryUtils_1.12.0.tgz
macOS Binary (arm64) TrajectoryUtils_1.12.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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