TrajectoryGeometry

DOI: 10.18129/B9.bioc.TrajectoryGeometry  

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

This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns

Bioconductor version: 3.16

Given a time series or pseudo-times series of gene expression data, we might wish to know: Do the changes in gene expression in these data exhibit directionality? Are there turning points in this directionality. Do different subsets of the data move in different directions? This package uses spherical geometry to probe these sorts of questions. In particular, if we are looking at (say) the first n dimensions of the PCA of gene expression, directionality can be detected as the clustering of points on the (n-1)-dimensional sphere.

Author: Michael Shapiro [aut, cre]

Maintainer: Michael Shapiro <michael.shapiro at crick.ac.uk>

Installation

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

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

BiocManager::install("TrajectoryGeometry")

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("TrajectoryGeometry")

 

HTML	R Script	SingleCellTrajectoryAnalysis
HTML	R Script	TrajectoryGeometry
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BiologicalQuestion, GeneExpression, SingleCell, Software, StatisticalMethod
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	MIT + file LICENSE
Depends	R (>= 4.1)
Imports	pracma, rgl, ggplot2, stats, methods
LinkingTo
Suggests	dplyr, knitr, RColorBrewer, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	TrajectoryGeometry_1.6.0.tar.gz
Windows Binary	TrajectoryGeometry_1.6.0.zip
macOS Binary (x86_64)	TrajectoryGeometry_1.6.0.tgz
macOS Binary (arm64)	TrajectoryGeometry_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TrajectoryGeometry
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TrajectoryGeometry
Bioc Package Browser	https://code.bioconductor.org/browse/TrajectoryGeometry/
Package Short Url	https://bioconductor.org/packages/TrajectoryGeometry/
Package Downloads Report	Download Stats