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TrajectoryUtils

This is the development version of TrajectoryUtils; for the stable release version, see TrajectoryUtils.

Single-Cell Trajectory Analysis Utilities


Bioconductor version: Development (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 gmail.com>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews GeneExpression, SingleCell, Software
Version 1.11.1
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
See More
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_1.11.1.tar.gz
Windows Binary TrajectoryUtils_1.11.1.zip
macOS Binary (x86_64) TrajectoryUtils_1.11.1.tgz
macOS Binary (arm64) TrajectoryUtils_1.11.1.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