U-Chrom

Universal Chromatin structure data analysis toolkit.

U-Chrom provides a unified framework for 3D chromatin structure analysis. The core data structure is a structure table — genomic bins mapped to 3D coordinates (chrom, start, end, x, y, z) — which can be obtained from either sequencing-based data (Hi-C, Dip-C) via 3D reconstruction, or imaging-based data (ORCA, MERFISH, DNA seqFISH+) via chromatin tracing.

On top of this common interface, U-Chrom implements:

  • Reconstruction from sparse Hi-C contacts (Nuc Dynamics, GEM, MDS/SMACOF)

  • Structure identification — loops (ArcFISH-style per-axis F-test), TADs (directionality index), compartments (placeholder)

  • Geometric features — distance matrices, contact frequency, radius of gyration

  • Interactive 3D browser built on PyVista + PyQt5

  • Population-level aggregation plots (median distance matrix, contact map, Rg histogram)

Quick start

pip install u-chrom

from uchrom import ChromData

# Import FOF-CT imaging data
cd = ChromData.from_fofct("example-data/core.csv")

# ArcFISH-style loop calling (GPU-accelerated)
from uchrom.strc.loop import call_loops_axiswise_f
loops = call_loops_axiswise_f(cd, chrom="chr17", device="auto")

# Persist
cd.write("data.h5cd")

Launch the interactive 3D browser:

python -m uchrom.browser data.h5cd

Getting started

Tutorials — Core & I/O

Tutorials — Reconstruction (recon)

Tutorials — Imaging & tracing (im)

Tutorials — Structure identification (strc)

Tutorials — Embedding (emb)

User guide

API reference

Project