GlycoForge generates realistic glycomics data under known ground truth for rigorous method benchmarking

Abstract Quantifying all complex carbohydrates in a sample produces glycomics data, which constitutes compositional data and is stymied by biosynthetic dependencies between glycans, requiring dedicated analytic workflows. Properly assessing such methods frequently requires simulated data with known ground truths and injectable effects. However, simulating glycomics data, especially with control over effects and biases, is still unsolved. Here, we present GlycoForge, a feature-complete solution for simulating comparative glycomics data. GlycoForge supports simulating fully synthetic glycomics data, with specified motif-level effects, drawn from Dirichlet distributions, and templated simulations based on real-world data. We further support the injection of batch effects, both mean and variance shifts, via center-log ratio transformations to maintain compositional closure, and realistic missing data simulation. We showcase the utility of GlycoForge by evaluating batch effect correction algorithms for glycomics data, with automated guidelines for when to use such methods on real-world data. GlycoForge is available as an open-access Python package at https://github.com/BojarLab/GlycoForge. Competing Interest Statement D.B. is consulting on glycobiology-related topics via SweetSense Analytics AB. The remaining authors declare no competing interests.