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Bioconductor - mia (development version)

mia

This is the development version of mia; for the stable release version, see mia.

Microbiome analysis

Bioconductor version: Development (3.22)

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.

Author: Tuomas Borman [aut, cre] ORCID: 0000-0002-8563-8884 , Felix G.M. Ernst [aut] ORCID: 0000-0001-5064-0928 , Sudarshan A. Shetty [aut] ORCID: 0000-0001-7280-9915 , Leo Lahti [aut] ORCID: 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: 0000-0003-2406-1978 , Chouaib Benchraka [ctb], Akewak Jeba [ctb] ORCID: 0009-0007-1347-7552 , Himmi Lindgren [ctb], Noah De Gunst [ctb], Théotime Pralas [ctb], Shadman Ishraq [ctb], Eineje Ameh [ctb], Artur Sannikov [ctb], Hervé Pagès [ctb], Rajesh Shigdel [ctb], Katariina Pärnänen [ctb], Pande Erawijantari [ctb], Danielle Callan [ctb], Sam Hillman [ctb], Jesse Pasanen [ctb]

Maintainer: Tuomas Borman <tuomas.v.borman at utu.fi>

Citation (from within R, enter citation("mia")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("mia")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("mia")
Details biocViews DataImport, Microbiome, Software Version 1.17.5 In Bioconductor since BioC 3.13 (R-4.1) (4 years) License Artistic-2.0 | file LICENSE 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, rbiom, rlang, S4Vectors, scater, scuttle, stats, stringr, tibble, tidyr, utils, vegan, Rcpp System Requirements URL https://github.com/microbiome/mia Bug Reports https://github.com/microbiome/mia/issues See More Suggests ade4, BiocStyle, biomformat, dada2, knitr, mediation, miaViz, microbiomeDataSets, NMF, patchwork, philr, phyloseq, reldist, rhdf5, rmarkdown, testthat, topicdoc, topicmodels, yaml Linking To Rcpp Enhances Depends On Me miaViz Imports Me dar, iSEEtree, lefser, MGnifyR, miaDash, curatedMetagenomicData Suggests Me ANCOMBC, HoloFoodR, miaSim, philr, bugphyzz, MicrobiomeBenchmarkData, MiscMetabar Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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