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TrajectoryGeometry

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

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

Bioconductor version: Development (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

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

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

Details

biocViews BiologicalQuestion, GeneExpression, SingleCell, Software, StatisticalMethod
Version 1.9.0
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
Linking To
Suggests dplyr, knitr, RColorBrewer, rmarkdown
System Requirements
Enhances
URL
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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_1.9.0.tar.gz
Windows Binary TrajectoryGeometry_1.9.0.zip
macOS Binary (x86_64) TrajectoryGeometry_1.9.0.tgz
macOS Binary (arm64) TrajectoryGeometry_1.9.0.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/
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