PanVizGenerator

DOI: 10.18129/B9.bioc.PanVizGenerator    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.14 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

Bioconductor version: Release (3.14)

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>

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")

 

HTML	R Script	Creating PanViz visualizations with PanVizGenerator
PDF		Reference Manual
Text		NEWS

Details

biocViews	ComparativeGenomics, GUI, Software, Visualization
Version	1.22.0
In Bioconductor since	BioC 3.3 (R-3.3) (6 years)
License	GPL (>= 2)
Depends	methods
Imports	shiny, tools, jsonlite, pcaMethods, FindMyFriends, igraph, stats, utils
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat, digest
SystemRequirements
Enhances
URL	https://github.com/thomasp85/PanVizGenerator
BugReports	https://github.com/thomasp85/PanVizGenerator/issues
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	PanVizGenerator_1.22.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)	PanVizGenerator_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PanVizGenerator
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PanVizGenerator
Package Short Url	https://bioconductor.org/packages/PanVizGenerator/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive