traviz

DOI: 10.18129/B9.bioc.traviz  

Trajectory functions for visualization and interpretation.

Bioconductor version: Release (3.16)

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>

Installation

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

 

HTML	R Script	ggplot2 + slingshot
HTML	R Script	traviz
PDF		Reference Manual

Details

biocViews	GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
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

Package Archives

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

Source Package	traviz_1.4.0.tar.gz
Windows Binary	traviz_1.4.0.zip (64-bit only)
macOS Binary (x86_64)	traviz_1.4.0.tgz
macOS Binary (arm64)	traviz_1.4.0.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