Structure calling

uchrom.strc calls chromatin structures from the 3-D data itself — from the distances between loci in many traces (chromatin tracing, DNA seqFISH+, a population of models), not from a contact map: loops (a per-axis F-test, ArcFISH), TADs (ArcFISH p-values, the directionality index), domains per allele (FISHnet) and A/B compartments. Every caller follows one calling convention: fn(cd, *, chrom=None, params=..., device="auto", key_added=..., copy=False); chrom=None runs every chromosome, results go to cd.intervals / cd.results with their provenance, and on a backed store the callers stream.

Structure	API
loops	uchrom.strc.loop.call_loops_axiswise_f, uc.tl.call_loops
TADs	uchrom.strc.tad.call_tads_by_pval, call_tads_di, uc.tl.call_tads
domains per trace / allele	uchrom.strc.tad.call_domains_fishnet
A/B compartments	uchrom.strc.comp.call_compartments_axes_pc, uc.tl.call_compartments
all of them, projected onto bins / spots	uchrom.strc.call_structures_multi, add_structural_features

The callers run on PyTorch (device="auto": CUDA, Apple MPS or CPU).

Tutorials

• Loop calling on chromatin tracing data
• TAD calling
• Single-allele domains with FISHnet
• A/B compartments from chromatin tracing

Guide

• Structure identification

API: loops, TADs, compartments, enrichment.