DESCRIPTION

Package: MGnifyR
Type: Package
Version: 1.3.0
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,
    urltools,
    utils,
    tidyjson
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
RoxygenNote: 7.3.1
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'