DESCRIPTION

Package: mia
Type: Package
Version: 1.15.4
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"),
             email = "felix.gm.ernst@outlook.com",
             comment = c(ORCID = "0000-0001-5064-0928")),
      person(given = "Sudarshan A.", family = "Shetty", role = c("aut"),
             email = "sudarshanshetty9@gmail.com",
             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"),
             email = "nolson@nist.gov"),
      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",
             email = "dbraccia@umd.edu", role=c("ctb")),
      person(given = "Basil", family = "Courbayre", role=c("ctb")),
      person(given = "Muluh", family = "Muluh", role=c("ctb")),
      person(given = "Giulio", family = "Benedetti", role=c("ctb")),
      person(given = c("Moritz", "Emanuel"), family = "Beber",
             email = "moritz.beber@igdore.org", role = c("ctb"),
             comment = c(ORCID = "0000-0003-2406-1978")),
      person(given = "Nitesh", family = "Turaga", role=c("ctb")),
      person(given = "Chouaib", family = "Benchraka", role=c("ctb")),
      person(given = "Akewak", family = "Jeba", role=c("ctb")),
      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")))
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,
    mediation,
    methods,
    rbiom,
    rlang,
    S4Vectors,
    scater,
    scuttle,
    stats,
    tibble,
    tidyr,
    utils,
    vegan
Suggests:
    ade4,
    BiocStyle,
    biomformat,
    dada2,
    knitr,
    miaViz,
    microbiomeDataSets,
    NMF,
    patchwork,
    phyloseq,
    reldist,
    rhdf5,
    rmarkdown,
    stringr,
    testthat,
    topicdoc,
    topicmodels,
    yaml
URL: https://github.com/microbiome/mia
BugReports: https://github.com/microbiome/mia/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr