mia

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

Microbiome analysis

Bioconductor version: Development (3.21)

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: ), Felix G.M. Ernst [aut] (ORCID: ), Sudarshan A. Shetty [aut] (ORCID: ), Leo Lahti [aut] (ORCID: ), 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], Giulio Benedetti [ctb], Moritz Emanuel Beber [ctb] (ORCID: ), Nitesh Turaga [ctb], Chouaib Benchraka [ctb], Akewak Jeba [ctb], 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]

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")

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	1.15.6
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 years)
License	Artistic-2.0 \| file LICENSE
Depends	R (>= 4.0), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment(>= 1.99.3)
Imports	ape, BiocGenerics, BiocParallel, Biostrings, bluster, DECIPHER, decontam, DelayedArray, DelayedMatrixStats, DirichletMultinomial, dplyr, IRanges, MASS, MatrixGenerics, mediation, methods, rbiom, rlang, S4Vectors, scater, scuttle, stats, tibble, tidyr, utils, vegan
System Requirements
URL	https://github.com/microbiome/mia
Bug Reports	https://github.com/microbiome/mia/issues

Suggests	ade4, BiocStyle, biomformat, dada2, knitr, miaViz, microbiomeDataSets, NMF, patchwork, phyloseq, reldist, rhdf5, rmarkdown, stringr, testthat, topicdoc, topicmodels, yaml
Linking To
Enhances
Depends On Me	miaViz
Imports Me	iSEEtree, MGnifyR, curatedMetagenomicData
Suggests Me	ANCOMBC, 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.

Source Package	mia_1.15.6.tar.gz
Windows Binary (x86_64)	mia_1.15.6.zip
macOS Binary (x86_64)	mia_1.15.6.tgz
macOS Binary (arm64)
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