DESCRIPTION

Package: mia
Type: Package
Version: 1.13.1
Authors@R:
    c(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 = "Tuomas", family = "Borman", role = c("aut", "cre"),
             email = "tuomas.v.borman@utu.fi",
             comment = c(ORCID = "0000-0002-8563-8884")),
      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")))
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),
    SummarizedExperiment,
    SingleCellExperiment,
    TreeSummarizedExperiment (>= 1.99.3),
    MultiAssayExperiment
Imports:
    methods,
    stats,
    utils,
    MASS,
    ape,
    decontam,
    vegan,
    BiocGenerics,
    S4Vectors,
    IRanges,
    Biostrings,
    DECIPHER,
    BiocParallel,
    DelayedArray,
    DelayedMatrixStats,
    scuttle,
    scater,
    DirichletMultinomial,
    rlang,
    dplyr,
    tibble,
    tidyr,
    bluster,
    MatrixGenerics,
    mediation
Suggests:
    testthat,
    knitr,
    patchwork,
    BiocStyle,
    yaml,
    phyloseq,
    dada2,
    stringr,
    biomformat,
    reldist,
    ade4,
    microbiomeDataSets,
    rmarkdown
URL: https://github.com/microbiome/mia
BugReports: https://github.com/microbiome/mia/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
VignetteBuilder: knitr