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
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make libgsl0-dev
        libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libuv1-dev libwebp-dev libxml2-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-16 07:34:47 UTC
RemoteUrl: https://github.com/bioc/mia
RemoteRef: HEAD
RemoteSha: fcd07419d8f9e4a1810f6d0a7ab7fe3b218bcaa3
NeedsCompilation: yes
Packaged: 2026-06-23 15:39:37 UTC; root
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>