ArcFISH: accurate and robust 3D genome feature discovery from chromatin tracing data#

ArcFISH is a computational tool to identify chromatin loops, TADs, and A/B compartments from chromatin tracing data, where the chromatin is in-situ hybridized by fluorescence probes and imaged using high-resolution microscopes (please see the 4DN data portal for a collection of available datasets).

ArcFISH is designed to handle the heterogenous measurement error in different axes. The workflow involves:

  1. Estimate a weight for each axis

  2. Filter our outliers and perform 1D bias normalization

  3. Process each axis separately:

    • Loops: F-test based on local background

    • TADs: F-test to compare inter-region and intra-region interactions

    • A/B compartments: second eigenvector

  4. Combine axis level information with weights estimated in step 1

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