microbiome
Microbiome Analytics
Bioconductor version: 3.24 · Package version: 1.35.1
Provides methods for microbiome data analysis and visualization, including compositional transformations, community profiling, diversity analysis, and exploration of taxonomic abundance data represented as phyloseq objects.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("microbiome")Details
| Maintainer | Leo Lahti <leo.lahti@iki.fi> |
| Author | Leo Lahti [aut, cre] (ORCID: <https://orcid.org/0000-0001-5537-637X>), Sudarshan Shetty [aut] (ORCID: <https://orcid.org/0000-0001-7280-9915>), Rasmus Hindström [ctb] (ORCID: <https://orcid.org/0009-0004-5731-178X>) |
| License | BSD_2_clause + file LICENSE |
| URL | http://microbiome.github.io/microbiome |
| Bug Reports | https://github.com/microbiome/microbiome/issues |
| Downloads rank | 2812 |
| Source branch | devel |
| biocViews | Metagenomics, Microbiome, Sequencing, Software, SystemsBiology |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | microbiome_1.35.1.tar.gz |
| Windows binary (x86_64) | microbiome_1.35.0.zip |
| macOS binary (arm64) | microbiome_1.35.0.tgz |
| macOS binary (x86_64) | microbiome_1.35.1.tgz |
Dependencies
Depends: R (>= 4.5.0), phyloseq, ggplot2
Imports: Biostrings, compositions, dplyr, methods, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan
Suggests: BiocGenerics, BiocStyle, Cairo, knitr, mia, rmarkdown, SummarizedExperiment, testthat, TreeSummarizedExperiment
Reverse dependencies
Depends On Me (1): TaxaNorm
Imports Me (3): benchdamic, DspikeIn, MicrobiomeSurv
Suggests Me (6): ANCOMBC, CrcBiomeScreen, dar, MeLSI, phylobar, zitools