metavizr

DOI: 10.18129/B9.bioc.metavizr  

R Interface to the metaviz web app for interactive metagenomics data analysis and visualization

Bioconductor version: Release (3.16)

This package provides Websocket communication to the metaviz web app (http://metaviz.cbcb.umd.edu) for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported (e.g., MRexperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as well.

Author: Hector Corrada Bravo [cre, aut], Florin Chelaru [aut], Justin Wagner [aut], Jayaram Kancherla [aut], Joseph Paulson [aut]

Maintainer: Hector Corrada Bravo <hcorrada 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("metavizr")

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("metavizr")

 

HTML	R Script	Introduction to metavizr
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GUI, ImmunoOncology, Infrastructure, Metagenomics, Software, Visualization
Version	1.21.0
In Bioconductor since	BioC 3.5 (R-3.4) (6 years)
License	MIT + file LICENSE
Depends	R (>= 3.4), metagenomeSeq(>= 1.17.1), methods, data.table, Biobase, digest
Imports	epivizr, epivizrData, epivizrServer, epivizrStandalone, vegan, GenomeInfoDb, phyloseq, httr
LinkingTo
Suggests	knitr, BiocStyle, matrixStats, msd16s(>= 0.109.1), etec16s, testthat, gss, ExperimentHub, tidyr, rmarkdown
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	metavizr_1.21.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/metavizr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/metavizr
Bioc Package Browser	https://code.bioconductor.org/browse/metavizr/
Package Short Url	https://bioconductor.org/packages/metavizr/
Package Downloads Report	Download Stats