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bioRxiv · 10.1101/2024.06.18.599627

FISHnet: Detecting chromatin domains in single-cell sequential Oligopaints imaging data

Patel, R.·Pham, K.·Chandrashekar, H.·Phillips-Cremins, J. E.
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Abstract

Sequential Oligopaints DNA FISH is an imaging technique that measures higher-order genome folding at single-allele resolution via multiplexed, probe-based tracing. Currently there is a paucity of algorithms to identify 3D genome features in sequential Oligopaints data. Here, we present FISHnet, a graph theory method based on optimization of network modularity to detect chromatin domains and boundaries in pairwise distance matrices. FISHnet uncovers cell type-specific domain-like folding patterns on single alleles, thus enabling future studies aiming to elucidate the role for single-cell folding variation on genome function.

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Patel, R., Pham, K., Chandrashekar, H., Phillips-Cremins, J. E.. 2024-06-18. FISHnet: Detecting chromatin domains in single-cell sequential Oligopaints imaging data. https://doi.org/10.1101/2024.06.18.599627

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