MGnifyR

R interface to EBI MGnify metagenomics resource


Bioconductor version: Release (3.19)

Utility package to facilitate integration and analysis of EBI MGnify data in R. The package can be used to import microbial data for instance into TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly compatible with miaverse framework.

Author: Tuomas Borman [aut, cre] , Ben Allen [aut], Leo Lahti [aut]

Maintainer: Tuomas Borman <tuomas.v.borman at utu.fi>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MGnifyR")

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("MGnifyR")
MGnifyR HTML R Script
MGnifyR, extended vignette HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataImport, Infrastructure, Metagenomics, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0 | file LICENSE
Depends R (>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment, SummarizedExperiment, BiocGenerics
Imports mia, ape, dplyr, httr, methods, plyr, reshape2, S4Vectors, urltools, utils, tidyjson
System Requirements
URL https://github.com/EBI-Metagenomics/MGnifyR
Bug Reports https://github.com/EBI-Metagenomics/MGnifyR/issues
See More
Suggests biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2, BiocStyle, miaViz, vegan, scater, phyloseq, magick
Linking To
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Package Archives

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

Source Package MGnifyR_1.0.0.tar.gz
Windows Binary (x86_64) MGnifyR_1.0.0.zip
macOS Binary (x86_64) MGnifyR_1.0.0.tgz
macOS Binary (arm64) MGnifyR_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MGnifyR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MGnifyR
Bioc Package Browser https://code.bioconductor.org/browse/MGnifyR/
Package Short Url https://bioconductor.org/packages/MGnifyR/
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