metavizr
This package is for version 3.9 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: 3.9
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("metavizr")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GUI, ImmunoOncology, Infrastructure, Metagenomics, Software, Visualization |
| Version | 1.8.0 |
| 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 |
See More
| Suggests | knitr, BiocStyle, matrixStats, msd16s(>= 0.109.1), etec16s, testthat, gss, curatedMetagenomicData |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | metavizr_1.8.0.tar.gz |
| Windows Binary | metavizr_1.8.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | metavizr_1.8.0.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 3.9 | Source Archive |