mia

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

Microbiome analysis

Bioconductor version: Development (3.23)

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], Eetu Tammi [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 "4.6") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Microbiome, Software
Version	1.19.0
In Bioconductor since	BioC 3.13 (R-4.1) (4.5 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, methods, rbiom, rlang, S4Vectors, scater, scuttle, stats, stringr, tibble, tidyr, utils, vegan, Rcpp
System Requirements
URL	https://microbiome.github.io/mia/ https://github.com/microbiome/mia
Bug Reports	https://github.com/microbiome/mia/issues

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
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/mia/
Package Downloads Report	Download Stats