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bioRxiv · 10.64898/2026.01.19.700311

UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity

Liu, J.·Gibcus, J. H.·Dekker, J.
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Abstract

Chromatin loop calling from chromatin interaction data often exhibits substantial variability across related samples. We present UnionLoops, a computational workflow for chromatin loop calling across multiple related samples. UnionLoops integrates information across datasets to determine positions and dataset-specificity of looping interactions. It constructs a unified candidate loop set, applies consistent filtering and aggregation, and evaluates loop support across samples. We demonstrate that UnionLoops increases sensitivity for detecting shared chromatin loops, reduces spurious sample-specific calls, and improves concordance with independent genomic features, including CTCF and cohesin occupancy. UnionLoops enables improved biological interpretation of chromatin loop organization and dynamics across related conditions.

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Liu, J., Gibcus, J. H., Dekker, J.. 2026-01-20. UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity. https://doi.org/10.64898/2026.01.19.700311

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