microbiome
This is the released version of microbiome; for the devel version, see microbiome.
All Bioconductor versions of microbiome
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6
Microbiome Analytics
Bioconductor version: 3.23 · Package version: 1.34.0
Utilities for microbiome analysis.
Author: Leo Lahti [aut, cre] 
, Sudarshan Shetty [aut]
Maintainer: Leo Lahti <leo.lahti at iki.fi>
Citation
From within R, enter citation("microbiome"):
Leo Lahti, Sudarshan Shetty. microbiome: Microbiome Analytics. doi:10.18129/B9.bioc.microbiome, R package version 1.34.0, https://bioconductor.org/packages/microbiome.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("microbiome")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.34.0 |
| License | BSD_2_clause + file LICENSE |
| URL | http://microbiome.github.io/microbiome |
| Bug Reports | https://github.com/microbiome/microbiome/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.6 (R-3.4) (8 years) |
| Downloads rank | 165 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Metagenomics, Microbiome, Sequencing, Software, SystemsBiology |
| Package Short Url | https://bioconductor.org/packages/microbiome/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("microbiome")| Introduction to the microbiome R package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | microbiome_1.34.0.tar.gz |
| Windows binary (x86_64) | microbiome_1.34.0.zip |
| macOS binary (arm64) | microbiome_1.34.0.tgz |
| macOS binary (x86_64) | microbiome_1.34.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/microbiome |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/microbiome |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 3.6.0), phyloseq, ggplot2
Imports: Biostrings, compositions, dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan
Suggests: BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat
Reverse dependencies
Depends On Me (1): TaxaNorm
Imports Me (3): benchdamic, DspikeIn, MicrobiomeSurv
Suggests Me (5): ANCOMBC, CrcBiomeScreen, dar, MeLSI, zitools