We are pleased to announce that a fruitful collaboration with the Turku Data Science group and international collaborators from the University of Copenhagen, Denmark, and EMBL-EBI, United Kingdom has led to a publication in the Bioinformatics journal about the HoloFoodR R/Bioconductor package!
About the package
HoloFoodR is an R/Bioconductor package that provides streamlined access to the multi-omic HoloFood database (https://www.holofooddata.org). The retrieved data is available in MultiAssayExperiment and TreeSummarizedExperiment formats, enabling simple access to downstream analyses using thousands of packages from the R/Bioconductor ecosystem. We hope that the package will improve the accessibility to such valuable scientific data and will contribute to Open Science!
Links
The paper is available at https://doi.org/10.1093/bioinformatics/btaf605.
The package is on Bioconductor: https://doi.org/10.18129/B9.bioc.HoloFoodR.
The package comes with a case study available at https://ebi-metagenomics.github.io/HoloFoodR/articles/case_study.html.