PanVizGenerator

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see PanVizGenerator.

Generate PanViz visualisations from your pangenome

DOI: 10.18129/B9.bioc.PanVizGenerator

Bioconductor version: 3.13

PanViz is a JavaScript based visualisation tool for functionaly annotated pangenomes. PanVizGenerator is a companion for PanViz that facilitates the necessary data preprocessing step necessary to create a working PanViz visualization. The output is fully self-contained so the recipient of the visualization does not need R or PanVizGenerator installed.

Author: Thomas Lin Pedersen

Maintainer: Thomas Lin Pedersen <thomasp85 at gmail.com>

Citation (from within R, enter citation("PanVizGenerator")):

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("PanVizGenerator")

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("PanVizGenerator")

Creating PanViz visualizations with PanVizGenerator HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ComparativeGenomics, GUI, Software, Visualization

Version 1.20.0

In Bioconductor since BioC 3.3 (R-3.3) (8 years)

License GPL (>= 2)

Depends methods

Imports shiny, tools, jsonlite, pcaMethods, FindMyFriends, igraph, stats, utils

System Requirements

URL https://github.com/thomasp85/PanVizGenerator

Bug Reports https://github.com/thomasp85/PanVizGenerator/issues

Suggests BiocStyle, knitr, rmarkdown, testthat, digest

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 PanVizGenerator_1.20.0.tar.gz

Windows Binary PanVizGenerator_1.20.0.zip

macOS 10.13 (High Sierra) PanVizGenerator_1.20.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/PanVizGenerator

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PanVizGenerator

Bioc Package Browser https://code.bioconductor.org/browse/PanVizGenerator/

Package Short Url https://bioconductor.org/packages/PanVizGenerator/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.13 Source Archive