mia

DOI: 10.18129/B9.bioc.mia    

Microbiome analysis

Bioconductor version: Release (3.13)

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, cre] , Sudarshan Shetty [aut] , Tuomas Borman [aut] , 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: Felix G.M. Ernst <felix.gm.ernst at outlook.com>

Citation (from within R, enter citation("mia")):

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML R Script mia
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews DataImport, Microbiome, Software
Version 1.0.2
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
License Artistic-2.0 | file LICENSE
Depends R (>= 4.1), SummarizedExperiment, SingleCellExperiment, TreeSummarizedExperiment(>= 1.99.3)
Imports methods, stats, utils, MASS, ape, decontam, vegan, BiocGenerics, S4Vectors, IRanges, Biostrings, DECIPHER, BiocParallel, DelayedArray, DelayedMatrixStats, scuttle, scater, DirichletMultinomial, rlang, dplyr, tibble, tidyr
LinkingTo
Suggests testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2, stringr, biomformat, reldist, ade4, microbiomeDataSets, rmarkdown
SystemRequirements
Enhances
URL https://github.com/microbiome/mia
BugReports https://github.com/microbiome/mia/issues
Depends On Me miaViz
Imports Me
Suggests Me curatedMetagenomicData
Links To Me
Build Report  

Package Archives

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

Source Package mia_1.0.2.tar.gz
Windows Binary mia_1.0.2.zip (32- & 64-bit)
macOS 10.13 (High Sierra) mia_1.0.2.tgz
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
Old Source Packages for BioC 3.13 Source Archive

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