Welcome to the new bioconductor.org!

traviz

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

Trajectory functions for visualization and interpretation.


Bioconductor version: Development (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 (from within R, enter citation("traviz")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("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")
ggplot2 + slingshot HTML R Script
traviz HTML R Script
Reference Manual PDF

Details

biocViews GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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_1.9.0.tar.gz
Windows Binary traviz_1.9.0.zip
macOS Binary (x86_64) traviz_1.9.0.tgz
macOS Binary (arm64)
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