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

R interface to EBI MGnify metagenomics resource

Bioconductor version: Development (3.20)

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>

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


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

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


To view documentation for the version of this package installed in your system, start R and enter:

MGnifyR HTML R Script
MGnifyR, extended vignette HTML R Script
Reference Manual PDF


biocViews DataImport, Infrastructure, Metagenomics, Software
Version 1.1.0
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
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Suggests biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2, BiocStyle, miaViz, vegan, scater, phyloseq, magick
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Follow Installation instructions to use this package in your R session.

Source Package MGnifyR_1.1.0.tar.gz
Windows Binary
macOS Binary (x86_64) MGnifyR_1.1.0.tgz
macOS Binary (arm64) MGnifyR_1.1.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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