microbiome

This is the development version of microbiome; for the stable release version, see microbiome.

All versions

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: Development (3.24)

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.

Author: Leo Lahti [aut, cre] ORCID: 0000-0001-5537-637X , Sudarshan Shetty [aut] ORCID: 0000-0001-7280-9915 , Rasmus Hindström [ctb] ORCID: 0009-0004-5731-178X

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 1.35.1, 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")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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 with TreeSummarizedExperiment	HTML	R Script
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	1.35.1
In Bioconductor since	BioC 3.6 (R-3.4) (9 years)
License	BSD_2_clause + file LICENSE
Depends	R (>= 4.5.0), phyloseq, ggplot2
Imports	Biostrings, compositions, dplyr, methods, 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, mia, rmarkdown, SummarizedExperiment, testthat, TreeSummarizedExperiment
Linking To
Enhances
Depends On Me	TaxaNorm
Imports Me	benchdamic, DspikeIn, MicrobiomeSurv
Suggests Me	ANCOMBC, CrcBiomeScreen, dar, MeLSI, phylobar, zitools
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow 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 (64-bit only)
macOS Binary (big-sur-x86_64)	microbiome_1.35.1.tgz
macOS Binary (sonoma-arm64)	microbiome_1.35.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/microbiome
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/microbiome
Package Short Url	https://bioconductor.org/packages/microbiome/
Package Downloads Report	Download Stats