traviz

DOI: 10.18129/B9.bioc.traviz    

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")

 

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

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  

Package Archives

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

Source Package traviz_0.99.07.tar.gz
Windows Binary traviz_0.99.07.zip
macOS 10.13 (High Sierra) traviz_0.99.07.tgz
Source Repository git clone https://git.bioconductor.org/packages/traviz
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/traviz
Package Short Url https://bioconductor.org/packages/traviz/
Package Downloads Report Download Stats

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