Package: mia
Type: Package
Version: 1.19.2
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 = "Felix G.M.", family = "Ernst", role = c("aut"),
             comment = c(ORCID = "0000-0001-5064-0928")),
      person(given = "Sudarshan A.", family = "Shetty", role = c("aut"),
             comment = c(ORCID = "0000-0001-7280-9915")),
      person(given = "Leo", family = "Lahti", role = c("aut"),
             email = "leo.lahti@iki.fi",
             comment = c(ORCID = "0000-0001-5537-637X")),
      person(given = "Yang", family = "Cao", role = c("ctb")),
      person(given = "Nathan D.", family = "Olson", role = c("ctb")),
      person(given = "Levi", family = "Waldron", role = c("ctb")),
      person(given = "Marcel", family = "Ramos", role = c("ctb")),
      person(given = "Héctor", family = "Corrada Bravo", role = c("ctb")),
      person(given = "Jayaram", family = "Kancherla", role=c("ctb")),
      person(given = "Domenick", family = "Braccia", role=c("ctb")),
      person(given = "Basil", family = "Courbayre", role=c("ctb")),
      person(given = "Geraldson", family = "Muluh", role=c("ctb")),
      person(given = "Giulio", family = "Benedetti", role=c("ctb")),
      person(given = c("Moritz", "Emanuel"), family = "Beber", role = c("ctb"),
             comment = c(ORCID = "0000-0003-2406-1978")),
      person(given = "Chouaib", family = "Benchraka", role=c("ctb")),
      person(given = "Akewak", family = "Jeba", role=c("ctb"),
             comment = c(ORCID = "0009-0007-1347-7552")),
      person(given = "Himmi", family = "Lindgren", role=c("ctb")),
      person(given = "Noah", family = "De Gunst", role=c("ctb")),
      person(given = "Théotime", family = "Pralas", role=c("ctb")),
      person(given = "Shadman", family = "Ishraq", role=c("ctb")),
      person(given = "Eineje", family = "Ameh", role=c("ctb")),
      person(given = "Artur", family = "Sannikov", role=c("ctb")),
      person(given = "Hervé", family = "Pagès", role=c("ctb")),
      person(given = "Rajesh", family = "Shigdel", role=c("ctb")),
      person(given = "Katariina", family = "Pärnänen", role=c("ctb")),
      person(given = "Pande", family = "Erawijantari", role=c("ctb")),
      person(given = "Danielle", family = "Callan", role=c("ctb")),
      person(given = "Sam", family = "Hillman", role=c("ctb")),
      person(given = "Jesse", family = "Pasanen", role=c("ctb")),
      person(given = "Eetu", family = "Tammi", role=c("ctb")))
Title: Microbiome analysis
Description:
    mia implements tools for microbiome analysis based on the
    SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment
    infrastructure. Data wrangling and analysis in the context of taxonomic data
    is the main scope. Additional functions for common task are implemented such
    as community indices calculation and summarization.
biocViews: Microbiome, Software, DataImport
License: Artistic-2.0 | file LICENSE
Encoding: UTF-8
LazyData: false
Depends:
    R (>= 4.0),
    MultiAssayExperiment,
    SingleCellExperiment,
    SummarizedExperiment,
    TreeSummarizedExperiment (>= 1.99.3)
Imports:
    ape,
    BiocGenerics,
    BiocParallel,
    Biostrings,
    bluster,
    DECIPHER,
    decontam,
    DelayedArray,
    DelayedMatrixStats,
    DirichletMultinomial,
    dplyr,
    IRanges,
    MASS,
    MatrixGenerics,
    methods,
    ecodive,
    rlang,
    S4Vectors,
    scater,
    scuttle,
    stats,
    stringr,
    tibble,
    tidyr,
    utils,
    vegan,
    Rcpp
Suggests:
    ade4,
    BiocStyle,
    biomformat,
    dada2,
    knitr,
    mediation,
    miaTime,
    miaViz,
    microbiomeDataSets,
    NMF,
    patchwork,
    philr,
    phyloseq,
    reldist,
    rhdf5,
    rmarkdown,
    testthat,
    topicdoc,
    topicmodels,
    yaml
LinkingTo:
    Rcpp
URL: https://microbiome.github.io/mia/, https://github.com/microbiome/mia
BugReports: https://github.com/microbiome/mia/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/mia
git_branch: devel
git_last_commit: 3645a0c
git_last_commit_date: 2025-12-09
Repository: Bioconductor 3.23
