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

Jiangyuan Liu·Johan H Gibcus·Job Dekker
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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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ChromatinCCCTC-Binding FactorWorkflowHumansAnimalsCohesinsSoftwareSensitivity and SpecificityChromosomal Proteins, Non-HistoneCell Cycle ProteinsJournal Article

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Jiangyuan Liu, Johan H Gibcus, Job Dekker. 2026-06-20. UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity.. https://doi.org/10.1186/s13059-026-04169-w

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