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mia

Microbiome analysis

Bioconductor version: Release (3.17)

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], Héctor Corrada Bravo [ctb], Jayaram Kancherla [ctb], Domenick Braccia [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 "4.3") and enter: 

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

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")
mia HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataImport, Microbiome, Software
Version 1.8.0
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
Linking To
Suggests testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2, stringr, biomformat, reldist, ade4, microbiomeDataSets, rmarkdown
System Requirements
Enhances
URL https://github.com/microbiome/mia
Bug Reports https://github.com/microbiome/mia/issues
See More
Depends On Me miaViz
Imports Me ANCOMBC, curatedMetagenomicData
Suggests Me CBEA, miaSim, MicrobiomeBenchmarkData, philr
Links To Me
Build Report  

Package Archives

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

Source Package mia_1.8.0.tar.gz
Windows Binary mia_1.8.0.zip
macOS Binary (x86_64)
macOS Binary (arm64) mia_1.8.0.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/
Package Downloads Report Download Stats