Package: MGnifyR
Type: Package
Version: 1.9.1
Authors@R: 
    c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
             email = "tuomas.v.borman@utu.fi",
             comment = c(ORCID = "0000-0002-8563-8884")),
      person(given = "Ben", family = "Allen", role = c("aut"),
             email = "ben.allen@ncl.ac.uk"),
      person(given = "Leo", family = "Lahti", role = c("aut"),
             email = "leo.lahti@iki.fi",
             comment = c(ORCID = "0000-0001-5537-637X")))
Title: R interface to EBI MGnify metagenomics resource
Description: 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.
biocViews: Infrastructure, DataImport, Metagenomics, Microbiome,
        MicrobiomeData
License: Artistic-2.0 | file LICENSE
Encoding: UTF-8
Depends: R(>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment,
        SummarizedExperiment, BiocGenerics
Imports: mia, ape, dplyr, httr, methods, plyr, reshape2, S4Vectors,
        stats, urltools, utils
Suggests: biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2,
        BiocStyle, miaViz, vegan, scater, phyloseq, magick
URL: https://github.com/EBI-Metagenomics/MGnifyR
BugReports: https://github.com/EBI-Metagenomics/MGnifyR/issues
VignetteBuilder: knitr
Collate: 'utils.R' 'MgnifyClient.R' 'AllGenerics.R' 'AllClasses.R'
        'AllAccessors.R' 'MGnifyR.R' 'deprecate.R' 'doQuery.R'
        'getData.R' 'getFile.R' 'getMetadata.R' 'getResult.R'
        'searchAnalysis.R'
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: cmake libglpk-dev make libgsl0-dev libicu-dev
        libuv1-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-19 08:02:40 UTC
RemoteUrl: https://github.com/bioc/MGnifyR
RemoteRef: HEAD
RemoteSha: 60edae14f4438ffab5d05c5f3cfc0ffd2b37e9d8
NeedsCompilation: no
Packaged: 2026-10-19 21:36:24 UTC; root
Author: Tuomas Borman [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-8563-8884>),
  Ben Allen [aut],
  Leo Lahti [aut] (ORCID: <https://orcid.org/0000-0001-5537-637X>)
Maintainer: Tuomas Borman <tuomas.v.borman@utu.fi>
Built: R 4.6.1; ; 2026-10-19 21:38:36 UTC; windows
