mia
Microbiome analysis
Bioconductor version: 3.23 · Package version: 1.20.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("mia")Details
| Maintainer | Tuomas Borman <tuomas.v.borman@utu.fi> |
| Author | Tuomas Borman [aut, cre] (ORCID: <https://orcid.org/0000-0002-8563-8884>), Felix G.M. Ernst [aut] (ORCID: <https://orcid.org/0000-0001-5064-0928>), Sudarshan A. Shetty [aut] (ORCID: <https://orcid.org/0000-0001-7280-9915>), Leo Lahti [aut] (ORCID: <https://orcid.org/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: <https://orcid.org/0000-0003-2406-1978>), Chouaib Benchraka [ctb], Akewak Jeba [ctb] (ORCID: <https://orcid.org/0009-0007-1347-7552>), Himmi Lindgren [ctb], Noah De Gunst [ctb], Théotime Pralas [ctb], Shadman Ishraq [ctb], Eineje Ameh [ctb], Artur Sannikov [ctb] (ORCID: <https://orcid.org/0000-0001-7765-123X>), Hervé Pagès [ctb], Rajesh Shigdel [ctb], Katariina Pärnänen [ctb], Pande Erawijantari [ctb], Danielle Callan [ctb], Sam Hillman [ctb], Jesse Pasanen [ctb], Eetu Tammi [ctb], Aituar Bektanov [ctb], Rasmus Hindström [ctb] |
| License | Artistic-2.0 | file LICENSE |
| URL | https://microbiome.github.io/mia/, https://github.com/microbiome/mia |
| Bug Reports | https://github.com/microbiome/mia/issues |
| Downloads rank | 2250 |
| Source branch | RELEASE_3_23 |
| biocViews | DataImport, Microbiome, Software |
Documentation
Download
Dependencies
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, ecodive, rlang, S4Vectors, scater, stats, stringr, tibble, tidyr, utils, vegan, Rcpp
LinkingTo: Rcpp
Suggests: ade4, BiocStyle, biomformat, dada2, knitr, mediation, miaTime, miaViz, microbiomeDataSets, NMF, patchwork, philr, phyloseq, reldist, rhdf5, rmarkdown, scuttle, testthat, topicdoc, topicmodels, yaml