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Bioconductor - MGnifyR (development version)

MGnifyR

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

R interface to EBI MGnify metagenomics resource

Bioconductor version: Development (3.22)

Utility package to facilitate integration and analysis of EBI MGnify data in R. The package can be used to import microbial data for instance into TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly compatible with miaverse framework.

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")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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 biocViews DataImport, Infrastructure, Metagenomics, Microbiome, MicrobiomeData, Software Version 1.5.0 In Bioconductor since BioC 3.19 (R-4.4) (1 year) License Artistic-2.0 | file LICENSE Depends R (>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment, SummarizedExperiment, BiocGenerics Imports mia, ape, dplyr, httr, methods, plyr, reshape2, S4Vectors, urltools, utils, tidyjson System Requirements URL https://github.com/EBI-Metagenomics/MGnifyR Bug Reports https://github.com/EBI-Metagenomics/MGnifyR/issues See More Suggests biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2, BiocStyle, miaViz, vegan, scater, phyloseq, magick Linking To Enhances Depends On Me Imports Me Suggests Me HoloFoodR Links To Me Build Report Build Report Package Archives

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

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