mia

Microbiome analysis

Bioconductor version: Release (3.19)

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], Basil Courbayre [ctb], Muluh Muluh [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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Microbiome, Software
Version	1.12.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 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, bluster, MatrixGenerics
System Requirements
URL	https://github.com/microbiome/mia
Bug Reports	https://github.com/microbiome/mia/issues

Suggests	testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2, stringr, biomformat, reldist, ade4, microbiomeDataSets, rmarkdown
Linking To
Enhances
Depends On Me	miaViz
Imports Me	ANCOMBC, MGnifyR, dar, curatedMetagenomicData
Suggests Me	CBEA, miaSim, philr, MicrobiomeBenchmarkData, MiscMetabar
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	mia_1.12.0.tar.gz
Windows Binary (x86_64)	mia_1.12.0.zip
macOS Binary (x86_64)	mia_1.12.0.tgz
macOS Binary (arm64)	mia_1.12.0.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