DOI: 10.18129/B9.bioc.mia  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see mia.

Microbiome analysis

Bioconductor version: 3.16

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: Felix G.M. Ernst [aut] , Sudarshan A. Shetty [aut] , Tuomas Borman [aut, cre] , Leo Lahti [aut] , Yang Cao [ctb], Nathan D. Olson [ctb], Levi Waldron [ctb], Marcel Ramos [ctb], H├ęctor Corrada Bravo [ctb], Jayaram Kancherla [ctb], Domenick Braccia [ctb]

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

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biocViews DataImport, Microbiome, Software
Version 1.6.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License Artistic-2.0 | file LICENSE
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
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
Depends On Me miaViz
Imports Me ANCOMBC, curatedMetagenomicData
Suggests Me CBEA, MicrobiomeBenchmarkData, philr
Links To Me
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Source Package mia_1.6.0.tar.gz
Windows Binary mia_1.6.0.zip (64-bit only)
macOS Binary (x86_64) mia_1.6.0.tgz
macOS Binary (arm64) mia_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/mia
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/mia
Bioc Package Browser https://code.bioconductor.org/browse/mia/
Package Short Url https://bioconductor.org/packages/mia/
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