traviz
Trajectory functions for visualization and interpretation.
Bioconductor version: Release (3.19)
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("traviz")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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")| ggplot2 + slingshot | HTML | R Script |
| traviz | HTML | R Script |
| Reference Manual |
Details
| biocViews | GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0) |
| Imports | ggplot2, viridis, mgcv, SingleCellExperiment, slingshot, princurve, Biobase, methods, RColorBrewer, SummarizedExperiment, grDevices, graphics, rgl |
| System Requirements | |
| URL |
See More
| Suggests | scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors, rmarkdown, knitr |
| 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 | traviz_1.10.0.tar.gz |
| Windows Binary (x86_64) | traviz_1.10.0.zip (64-bit only) |
| macOS Binary (x86_64) | traviz_1.10.0.tgz |
| macOS Binary (arm64) | traviz_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/traviz |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/traviz |
| Bioc Package Browser | https://code.bioconductor.org/browse/traviz/ |
| Package Short Url | https://bioconductor.org/packages/traviz/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.19 | Source Archive |