Package: mia
Type: Package
Version: 1.21.3
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"),
             comment = c(ORCID = "0000-0001-7765-123X")),
      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")),
      person(given = "Aituar", family = "Bektanov", role=c("ctb")),
      person(given = "Rasmus", family = "Hindström", role=c("ctb")),
      person(given = "Sabuj", family = "Bhowmick", 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 (>= 4.1.0), 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, stats, stringr,
        tibble, tidyr, utils, vegan, Rcpp
Suggests: ade4, BiocStyle, biomformat, dada2, knitr, mediation,
        miaTime, miaViz, microbiomeDataSets, NMF, patchwork, philr,
        phyloseq, reldist, rhdf5, rmarkdown, scuttle, 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: fcd0741
git_last_commit_date: 2026-06-16
Repository: Bioconductor 3.24
Date/Publication: 2026-06-16
NeedsCompilation: yes
Packaged: 2026-06-16 22:44:46 UTC; biocbuild
Author: Tuomas Borman [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-8563-8884>),
  Felix G.M. Ernst [aut] (ORCID: <https://orcid.org/0000-0001-5064-0928>),
  Sudarshan A. Shetty [aut] (ORCID:
    <https://orcid.org/0000-0001-7280-9915>),
  Leo Lahti [aut] (ORCID: <https://orcid.org/0000-0001-5537-637X>),
  Yang Cao [ctb],
  Nathan D. Olson [ctb],
  Levi Waldron [ctb],
  Marcel Ramos [ctb],
  Héctor Corrada Bravo [ctb],
  Jayaram Kancherla [ctb],
  Domenick Braccia [ctb],
  Basil Courbayre [ctb],
  Geraldson Muluh [ctb],
  Giulio Benedetti [ctb],
  Moritz Emanuel Beber [ctb] (ORCID:
    <https://orcid.org/0000-0003-2406-1978>),
  Chouaib Benchraka [ctb],
  Akewak Jeba [ctb] (ORCID: <https://orcid.org/0009-0007-1347-7552>),
  Himmi Lindgren [ctb],
  Noah De Gunst [ctb],
  Théotime Pralas [ctb],
  Shadman Ishraq [ctb],
  Eineje Ameh [ctb],
  Artur Sannikov [ctb] (ORCID: <https://orcid.org/0000-0001-7765-123X>),
  Hervé Pagès [ctb],
  Rajesh Shigdel [ctb],
  Katariina Pärnänen [ctb],
  Pande Erawijantari [ctb],
  Danielle Callan [ctb],
  Sam Hillman [ctb],
  Jesse Pasanen [ctb],
  Eetu Tammi [ctb],
  Aituar Bektanov [ctb],
  Rasmus Hindström [ctb],
  Sabuj Bhowmick [ctb]
Maintainer: Tuomas Borman <tuomas.v.borman@utu.fi>
