metavizr

This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see metavizr.

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


Bioconductor version: 3.11

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 "4.0") 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")
Introduction to metavizr HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GUI, ImmunoOncology, Infrastructure, Metagenomics, Software, Visualization
Version 1.12.0
In Bioconductor since BioC 3.5 (R-3.4) (7 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
System Requirements
URL
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Suggests knitr, BiocStyle, matrixStats, msd16s(>= 0.109.1), etec16s, testthat, gss, curatedMetagenomicData
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Depends On Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package metavizr_1.12.0.tar.gz
Windows Binary metavizr_1.12.0.zip
macOS 10.13 (High Sierra) metavizr_1.12.0.tgz
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
Old Source Packages for BioC 3.11 Source Archive