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Bioconductor - HoloFoodR (development version)

HoloFoodR

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

R interface to EBI HoloFood resource

Bioconductor version: Development (3.22)

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")): 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("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")
Details biocViews DataImport, Infrastructure, Microbiome, MicrobiomeData, Software Version 1.3.1 In Bioconductor since BioC 3.20 (R-4.4) (0.5 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 See More 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 Package Archives

Follow Installation instructions to use this package in your R session.

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