Package: HoloFoodR 1.6.0

Tuomas Borman

HoloFoodR: R interface to EBI HoloFood resource

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.

Authors:Tuomas Borman [aut, cre], Artur Sannikov [aut], Leo Lahti [aut]

HoloFoodR_1.6.0.tar.gz
HoloFoodR_1.6.0.zip(r-4.7)HoloFoodR_1.6.0.zip(r-4.6)HoloFoodR_1.6.0.zip(r-4.5)
HoloFoodR_1.6.0.tgz(r-4.6-any)HoloFoodR_1.6.0.tgz(r-4.5-any)
HoloFoodR_1.6.0.tar.gz(r-4.7-any)HoloFoodR_1.6.0.tar.gz(r-4.6-any)
HoloFoodR_1.6.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
HoloFoodR/json (API)
NEWS

# Install 'HoloFoodR' in R:

install.packages('HoloFoodR', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ebi-metagenomics/holofoodr/issues

On BioConductor:HoloFoodR-1.7.0(bioc 3.24)HoloFoodR-1.6.0(bioc 3.23)

software infrastructure dataimport microbiome microbiomedata

4.78 score 2 stars 5 scripts 243 downloads 6 exports 66 dependencies

Last updated from:a27e366f64 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	228
linux-devel-x86_64	NOTE	326
source / vignettes	OK	430
linux-release-x86_64	NOTE	418
macos-release-arm64	NOTE	280
macos-oldrel-arm64	NOTE	264
windows-devel	NOTE	291
windows-release	NOTE	259
windows-oldrel	NOTE	296
wasm-release	OK	188

Exports:addMGnify doQuery getData getMetaboLights getMetaboLightsFile getResult

Dependencies:abind ape askpass BH Biobase BiocBaseUtils BiocGenerics BiocParallel Biostrings cli codetools cpp11 crayon curl DelayedArray digest dplyr formatR fs futile.logger futile.options generics GenomicRanges glue httr2 IRanges jsonlite lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats MultiAssayExperiment nlme openssl pillar pkgconfig purrr R6 rappdirs Rcpp rlang S4Arrays S4Vectors Seqinfo SingleCellExperiment snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tidytree treeio TreeSummarizedExperiment utf8 vctrs withr XVector yulab.utils

HoloFoodR: interface to HoloFoodR database

Rendered fromHoloFoodR.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2025-05-28
Started: 2024-02-26

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add results from MGnifyR to HoloFoodR results	addMGnify addMGnify,SummarizedExperiment,ANY-method addMGnify,SummarizedExperiment,MultiAssayExperiment-method addMGnify,SummarizedExperiment,SummarizedExperiment-method
Search HoloFood database for animals, genome catalogues, samples, or viral catalogues	doQuery
Get data from HoloFood database	getData
Get metabolomic data from MetaboLights database	getMetaboLights getMetaboLightsFile
Get data on samples from HoloFood database	getResult
'HoloFoodR' package	HoloFoodR-package HoloFoodR