Installation

From PyPI

pip install u-chrom

From source

git clone https://github.com/Nanguage/U-Chrom.git
cd U-Chrom
pip install -e .

Optional dependencies

Some workflows need heavier dependencies that are published as extras:

Extra	Installs	Needed for
browser	PyVista, pyvistaqt, VTK, PyQt5, qdarkgraystyle	python -m uchrom.browser
web	FastAPI, uvicorn	python -m uchrom.browser --web (browser in a web page)
hic	hic-straw	reading .hic files
anndata	anndata	ChromData.link_anndata / to_anndata, seqFISH RNA
multiome	mudata	ChromData.load_linked_mudata
umap	umap-learn	UMAP in uchrom.emb.embed_cells (PCA / t-SNE need only scikit-learn)
im	astropy	ChromData.from_pyhim_trace
snapfish	scikit-image	SnapFISH-IMPUTE (uchrom.im.impute)
emb / emb-full	FastHigashi / Higashi	uchrom.emb.higashi

pip install "u-chrom[browser]"
pip install "u-chrom[browser,hic,anndata]"   # several at once

GPU acceleration

The tensor-heavy steps (axis-wise variance cube, F-test, MDS) run through PyTorch on the best available device:

Device	Precision	Typical use
cuda	float64	NVIDIA desktop / server
mps	float32	Apple Silicon
cpu	float64	fallback

Pass device="auto" (the default) to pick automatically, or an explicit device name to pin. GPU support is optional — everything works on CPU.

Verifying the install

import uchrom
print(uchrom.__version__)

from uchrom import ChromData

If that works, the core package is usable. If you installed the browser extras:

python -m uchrom.browser --help