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metavizr

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

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

Bioconductor version: Release (3.17)

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>

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

Installation

To install this package, start R (version "4.3") 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

Reference Manual PDF

Details

biocViews GUI, ImmunoOncology, Infrastructure, Metagenomics, Software, Visualization
Version 1.24.0
In Bioconductor since BioC 3.5 (R-3.4) (6.5 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
Linking To
Suggests knitr, BiocStyle, matrixStats, msd16s(>= 0.109.1), etec16s, testthat, gss, ExperimentHub, tidyr, rmarkdown
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Follow Installation instructions to use this package in your R session.

Source Package
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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/
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