mia
This is thereleased version of mia; for the devel version, seemia.
Microbiome analysis
DOI: 10.18129/B9.bioc.mia
Bioconductor version: Release (3.22)
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("mia")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("mia")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport,Microbiome,Software |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (4.5 years) |
| License | Artistic-2.0 | fileLICENSE |
| Depends | R (>= 4.1.0),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 |
See More
| 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 | miaTime,miaViz |
| Imports Me | dar,iSEEtree,lefser,MGnifyR,miaDash,curatedMetagenomicData |
| Suggests Me | anansi,ANCOMBC,DspikeIn,HoloFoodR,miaSim,philr,bugphyzz,MicrobiomeBenchmarkData,MiscMetabar |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | mia_1.18.0.tar.gz |
| Windows Binary (x86_64) | mia_1.18.0.zip |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/mia/ |
| Package Short Url | https://bioconductor.org/packages/mia/ |
| Package Downloads Report | Download Stats |