This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see mia.
Bioconductor version: 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")
):
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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("mia")
HTML | R Script | mia |
Reference Manual | ||
Text | NEWS | |
Text | LICENSE |
biocViews | DataImport, Microbiome, Software |
Version | 1.8.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (2.5 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 |
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 | ANCOMBC, curatedMetagenomicData |
Suggests Me | CBEA, miaSim, MicrobiomeBenchmarkData, philr |
Links To Me | |
Build Report |
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 |
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