Package: HoloFoodR 1.1.1

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_1.1.1.tar.gz
HoloFoodR_1.1.1.zip(r-4.5)HoloFoodR_1.1.1.zip(r-4.4)
HoloFoodR_1.1.1.tgz(r-4.5-any)HoloFoodR_1.1.1.tgz(r-4.4-any)
HoloFoodR_1.1.1.tar.gz(r-4.5-noble)HoloFoodR_1.1.1.tar.gz(r-4.4-noble)
HoloFoodR_1.1.1.tgz(r-4.4-emscripten)
HoloFoodR.pdf |HoloFoodR.html✨
HoloFoodR/json (API)
NEWS

# Install 'HoloFoodR' in R:

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

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

On BioConductor:HoloFoodR-1.1.1(bioc 3.21)HoloFoodR-1.0.0(bioc 3.20)

software infrastructure dataimport microbiome microbiomedata

4.70 score 1 stars 6 scripts 109 downloads 6 exports 71 dependencies

Last updated 1 months agofrom:1f9b3fb177. Checks:1 OK, 6 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 29 2025
R-4.5-win	NOTE	Mar 29 2025
R-4.5-mac	NOTE	Mar 29 2025
R-4.5-linux	NOTE	Mar 29 2025
R-4.4-win	NOTE	Mar 29 2025
R-4.4-mac	NOTE	Mar 29 2025
R-4.4-linux	NOTE	Mar 29 2025

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 fansi formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr httr2 IRanges jsonlite lambda.r lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats mime MultiAssayExperiment nlme openssl pillar pkgconfig purrr R6 rappdirs Rcpp rlang S4Arrays S4Vectors SingleCellExperiment snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tidytree treeio TreeSummarizedExperiment UCSC.utils utf8 vctrs withr XVector yulab.utils

HoloFoodR: interface to HoloFoodR database

Rendered fromHoloFoodR.Rmdusingknitr::rmarkdownon Mar 29 2025.

Last update: 2024-11-25
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