GlyEnzEA: software and reproducibility workflow for enzyme-centered glycan-set enrichment
Abstract
GlyEnzEA supports enzyme-centered interpretation of glycomic changes by testing whether glycans associated with enzyme reactions change collectively. It matches reaction rules to candidate glycan topologies, constructs enzyme-centered sets of measured features, groups enzymes sharing identical sets, and tests each distinct set once. All enzymes sharing a tested set are reported. This archive preserves the R implementation, documented analysis workflow, source/test data, frozen API responses and reference outputs accompanying the manuscript “GlyEnzEA: reaction-informed enrichment of enzyme-centered glycan sets from glycomics data.” Evaluation uses an Mgat3-knockout mouse glycome and seven HEK293 perturbations. Enrichment describes reaction-associated structural changes at the resolution supported by the data; it does not directly measure enzyme activity. Source repository: https://github.com/matsui-lab/GlyEnzEA-paper. Exact source commit: 9dce64f5c374414c7549fa7d69a5a4d7fc871292. This deposit is a commit-identified snapshot prepared on 14 October 2026, not a tagged software release. All 529 retained source files are byte-identical to that commit. The ZIP also contains a README, MIT LICENSE, rights notice and SHA-256 manifest. The package contains run_all.R, renv.lock, R/, scripts/, data/, cache/, output/, provenance/ and selected reference figure/table assets. Manuscript drafts, redlines, exploratory artwork and submission administration files are omitted. The final journal submission PDFs are not part of this code/data archive. See README_Zenodo_MIT.txt for commands, scope and provenance. Archive integrity and retained-file identity were checked; the analyses were not rerun during packaging. The authors' original code is released under the MIT License. Third-party code, source tables and database inputs retain their original rights and conditions; MIT does not relicense those materials. The authors have confirmed permission to publish and redistribute the included data, including the Kizuka laboratory source tables. The development repository is private; this Zenodo deposit supplies the publicly distributable code and data snapshot.
