MGnifyR
This is thereleased version of MGnifyR; for the devel version, seeMGnifyR.
R interface to EBI MGnify metagenomics resource
Bioconductor version: Release (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("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 appropriateBioconductor 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 |
| MGnifyR, extended vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport,Infrastructure,Metagenomics,Microbiome,MicrobiomeData,Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (1.5 years) |
| License | Artistic-2.0 | fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | MGnifyR_1.6.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| 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 |