TrajectoryUtils

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see TrajectoryUtils.

Single-Cell Trajectory Analysis Utilities

Bioconductor version: 3.16

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 gmail.com>

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

Installation

To install this package, start R (version "4.2") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("TrajectoryUtils")

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

Documentation

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

browseVignettes("TrajectoryUtils")

Trajectory utilities HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, SingleCell, Software

Version 1.6.0

In Bioconductor since BioC 3.13 (R-4.1) (3 years)

License GPL-3

Depends SingleCellExperiment

Imports methods, stats, Matrix, igraph, S4Vectors, SummarizedExperiment

System Requirements

URL https://bioconductor.org/packages/TrajectoryUtils

Bug Reports https://github.com/LTLA/TrajectoryUtils/issues

Suggests BiocNeighbors, DelayedArray, DelayedMatrixStats, BiocParallel, testthat, knitr, BiocStyle, rmarkdown

Linking To

Enhances

Depends On Me slingshot, TSCAN

Imports Me condiments, singleCellTK, tradeSeq

Suggests Me

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package TrajectoryUtils_1.6.0.tar.gz

Windows Binary TrajectoryUtils_1.6.0.zip

macOS Binary (x86_64) TrajectoryUtils_1.6.0.tgz

macOS Binary (arm64) TrajectoryUtils_1.6.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/TrajectoryUtils

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TrajectoryUtils

Bioc Package Browser https://code.bioconductor.org/browse/TrajectoryUtils/

Package Short Url https://bioconductor.org/packages/TrajectoryUtils/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.16 Source Archive