MGnifyR

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see MGnifyR.

R interface to EBI MGnify metagenomics resource

Bioconductor version: 3.21

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 iD ORCID: 0000-0002-8563-8884 , Ben Allen [aut], Leo Lahti [aut] ORCID iD 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")
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")

MGnifyR HTML R Script

MGnifyR, extended vignette HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, Infrastructure, Metagenomics, Microbiome, MicrobiomeData, Software

Version 1.4.0

In Bioconductor since BioC 3.19 (R-4.4) (1.5 years)

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

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.

Source Package MGnifyR_1.4.0.tar.gz

Windows Binary (x86_64) MGnifyR_1.3.0.zip

macOS Binary (x86_64) MGnifyR_1.4.0.tgz

macOS Binary (arm64) MGnifyR_1.4.0.tgz

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

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

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

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

Package Downloads Report Download Stats