HoloFoodR

R interface to EBI HoloFood resource

Bioconductor version: 3.24 · Package version: 1.7.0

Utility package to facilitate integration and analysis of EBI HoloFood data in R. This package streamlines access to the resource, allowing for direct loading of data into formats optimized for downstream analytics.

Installation

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

BiocManager::install("HoloFoodR")

Details

Maintainer	Tuomas Borman <tuomas.v.borman@utu.fi>
Author	Tuomas Borman [aut, cre] (ORCID: <https://orcid.org/0000-0002-8563-8884>), Artur Sannikov [aut] (ORCID: <https://orcid.org/0000-0001-7765-123X>), Leo Lahti [aut] (ORCID: <https://orcid.org/0000-0001-5537-637X>)
License	Artistic-2.0 \| file LICENSE
URL	https://github.com/EBI-Metagenomics/HoloFoodR
Bug Reports	https://github.com/EBI-Metagenomics/HoloFoodR/issues
Downloads rank	320
Source branch	devel
biocViews	DataImport, Infrastructure, Microbiome, MicrobiomeData, Software

Documentation

HoloFoodR: interface to HoloFoodR database

Download

Follow the installation instructions to use this package in your R session.

Source package	HoloFoodR_1.7.0.tar.gz
Windows binary (x86_64)	HoloFoodR_1.7.0.zip
macOS binary (arm64)	HoloFoodR_1.7.0.tgz
macOS binary (x86_64)	HoloFoodR_1.7.0.tgz

Dependencies

Depends: R (>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment

Imports: dplyr, httr2, jsonlite, S4Vectors, stringi, stats, SummarizedExperiment, utils

Suggests: BiocStyle, DT, ggh4x, ggsignif, knitr, MGnifyR, mia, miaViz, MOFA2, patchwork, reticulate, rmarkdown, scater, shadowtext, testthat, UpSetR