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MGnifyR

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

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3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19

R interface to EBI MGnify metagenomics resource

DOI: 10.18129/B9.bioc.MGnifyR

Bioconductor version: Development (3.24)

MGnifyR is an R interface to MGnify, EBI's resource for the analysis of metagenomic, metatranscriptomic and amplicon data. It searches MGnify studies, samples and analyses with MGnify API v2, and fetches their taxonomic and functional profiles together with sample metadata. The data is returned as TreeSummarizedExperiment or MultiAssayExperiment, so that it can be analysed directly with Bioconductor microbiome tools.

Author: Tuomas Borman [aut, cre] ORCID: 0000-0002-8563-8884 , Ben Allen [aut], Leo Lahti [aut] ORCID: 0000-0001-5537-637X

Maintainer: Tuomas Borman <tuomas.v.borman at utu.fi>

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

Tuomas Borman, Ben Allen, Leo Lahti. MGnifyR: R interface to EBI MGnify metagenomics resource. doi:10.18129/B9.bioc.MGnifyR, R package version 1.9.1, https://bioconductor.org/packages/MGnifyR.

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("MGnifyR")

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("MGnifyR")

Details

Package Archives

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