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 (3.21)
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:
Maintainer: Tuomas Borman <tuomas.v.borman at utu.fi>
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")| MGnifyR | HTML | R Script |
| MGnifyR, extended vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, Infrastructure, Metagenomics, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 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 |
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 | iSEEtree |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MGnifyR_1.3.0.tar.gz |
| Windows Binary (x86_64) | MGnifyR_1.3.0.zip |
| macOS Binary (x86_64) | MGnifyR_1.3.0.tgz |
| macOS Binary (arm64) | |
| 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 |