OmicsLake: Versioned, Agent-Aware Data Lineage for R/Bioconductor Workflows

Abstract

OmicsLake is an R package for version-aware, dataset-level lineage in R/Bioconductor exploratory workflows. It associates stored versions with dependencies captured within tracked ref()-dplyr-save_as() pipelines or supplied explicitly, and can attach caller-supplied human or software-agent identifiers. Controlled tests recovered all ground-truth edges within the supported path and enabled explicit recovery of an overwritten tagged intermediate. OmicsLake 0.99.3 is MIT-licensed software available at https://github.com/matsui-lab/OmicsLake (tag v0.99.3); source, tests, and evaluation files are archived at https://doi.org/10.5281/zenodo.21391428. Supplementary Material accompanies this preprint.