microbiome

This is the released version of microbiome; for the devel version, see microbiome.

Microbiome Analytics

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DOI: 10.18129/B9.bioc.microbiome

Bioconductor version: Release (3.22)

Utilities for microbiome analysis.

Author: Leo Lahti [aut, cre] ORCID iD ORCID: 0000-0001-5537-637X , Sudarshan Shetty [aut] ORCID iD ORCID: 0000-0001-7280-9915

Maintainer: Leo Lahti <leo.lahti at iki.fi>

Citation (from within R, enter citation("microbiome")):

Installation

To install this package, start R (version "4.5") 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("microbiome")

microbiome R package HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Metagenomics, Microbiome, Sequencing, Software, SystemsBiology

Version 1.32.0

In Bioconductor since BioC 3.6 (R-3.4) (8 years)

License BSD_2_clause + file LICENSE

Depends R (>= 3.6.0), phyloseq, ggplot2

Imports Biostrings, compositions, dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils, vegan

System Requirements

URL http://microbiome.github.io/microbiome

Bug Reports https://github.com/microbiome/microbiome/issues

Suggests BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat

Linking To

Enhances

Depends On Me

Imports Me DspikeIn, MicrobiomeSurv

Suggests Me ANCOMBC, dar, zitools

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package microbiome_1.32.0.tar.gz

Windows Binary (x86_64) microbiome_1.31.4.zip

macOS Binary (x86_64) microbiome_1.32.0.tgz

macOS Binary (arm64) microbiome_1.32.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/microbiome

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/microbiome

Bioc Package Browser https://code.bioconductor.org/browse/microbiome/

Package Short Url https://bioconductor.org/packages/microbiome/

Package Downloads Report Download Stats