HoloFoodR

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20

R interface to EBI HoloFood resource

Bioconductor version: Development (3.24)

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.

Author: Tuomas Borman [aut, cre] ORCID: 0000-0002-8563-8884 , Artur Sannikov [aut] ORCID: 0000-0001-7765-123X , Leo Lahti [aut] ORCID: 0000-0001-5537-637X

Maintainer: Tuomas Borman <tuomas.v.borman at utu.fi>

Citation (from within R, enter citation("HoloFoodR")):

Tuomas Borman, Artur Sannikov, Leo Lahti. HoloFoodR: R interface to EBI HoloFood resource. doi:10.18129/B9.bioc.HoloFoodR, R package version 1.7.0, https://bioconductor.org/packages/HoloFoodR.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("HoloFoodR")

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("HoloFoodR")

HoloFoodR	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Infrastructure, Microbiome, MicrobiomeData, Software
Version	1.7.0
In Bioconductor since	BioC 3.20 (R-4.4) (2 years)
License	Artistic-2.0 \| file LICENSE
Depends	R (>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment
Imports	dplyr, httr2, jsonlite, S4Vectors, stringi, stats, SummarizedExperiment, utils
System Requirements
URL	https://github.com/EBI-Metagenomics/HoloFoodR
Bug Reports	https://github.com/EBI-Metagenomics/HoloFoodR/issues

Suggests	BiocStyle, DT, ggh4x, ggsignif, knitr, MGnifyR, mia, miaViz, MOFA2, patchwork, reticulate, rmarkdown, scater, shadowtext, testthat, UpSetR
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow 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 (big-sur-x86_64)	HoloFoodR_1.7.0.tgz
macOS Binary (sonoma-arm64)	HoloFoodR_1.7.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HoloFoodR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HoloFoodR
Package Short Url	https://bioconductor.org/packages/HoloFoodR/
Package Downloads Report	Download Stats