metavizr

DOI: 10.18129/B9.bioc.metavizr    

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

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

Bioconductor version: Development (3.14)

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 <hcorrada at gmail.com>, Florin Chelaru <florin.chelaru at gmail.com>, Justin Wagner <jwagner at cs.umd.edu>, Jayaram Kancherla <jayaram.kancherla at gmail.com>, Joseph Paulson <jpaulson at jimmy.harvard.edu>

Maintainer: Hector Corrada Bravo <hcorrada at gmail.com>

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

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("metavizr")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews GUI, ImmunoOncology, Infrastructure, Metagenomics, Software, Visualization
Version 1.17.0
In Bioconductor since BioC 3.5 (R-3.4) (4 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, curatedMetagenomicData
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
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/metavizr
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/metavizr
Package Short Url https://bioconductor.org/packages/metavizr/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: