This is the development version of traviz; to use it, please install the devel version of Bioconductor.
Trajectory functions for visualization and interpretation.
Bioconductor version: Development (3.14)
traviz provides a suite of functions to plot trajectory related objects from Bioconductor packages. It allows plotting trajectories in reduced dimension, as well as averge gene expression smoothers as a function of pseudotime. Asides from general utility functions, traviz also allows plotting trajectories estimated by Slingshot, as well as smoothers estimated by tradeSeq. Furthermore, it allows for visualization of Slingshot trajectories using ggplot2.
Author: Hector Roux de Bezieux [aut, ctb], Kelly Street [aut, ctb], Koen Van den Berge [aut, cre]
Maintainer: Koen Van den Berge <koen.vdberge at gmail.com>
Citation (from within R,
enter citation("traviz")):
Installation
To install this package, start R (version
“4.1”) and enter:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("traviz")
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("traviz")
Details
| biocViews | GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Version | 0.99.07 |
| In Bioconductor since | BioC 3.14 (R-4.1) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0) |
| Imports | ggplot2, viridis, mgcv, SingleCellExperiment, slingshot, princurve, Biobase, methods, RColorBrewer, SummarizedExperiment, grDevices, graphics, rgl |
| LinkingTo | |
| Suggests | scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors, rmarkdown, knitr |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
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Installation instructions to use this
package in your R session.
Read more here: Source link