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 (3.21)
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] (ORCID:
Maintainer: Michael Shapiro <michael.shapiro at crick.ac.uk>
citation("TrajectoryGeometry")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiologicalQuestion, GeneExpression, SingleCell, Software, StatisticalMethod |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1) |
| Imports | pracma, rgl, ggplot2, stats, methods |
| System Requirements | |
| URL |
See More
| Suggests | dplyr, knitr, RColorBrewer, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TrajectoryGeometry_1.15.0.tar.gz |
| Windows Binary (x86_64) | TrajectoryGeometry_1.15.0.zip (64-bit only) |
| macOS Binary (x86_64) | TrajectoryGeometry_1.15.0.tgz |
| macOS Binary (arm64) | TrajectoryGeometry_1.15.0.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 |