U-Chrom¶
Universal Chromatin: one toolkit for 3-D genome data from sequencing and imaging.
Single-cell Hi-C, spatial Hi-C, bulk Hi-C, chromatin tracing and DNA seqFISH+ all describe the
same thing — where loci sit relative to each other, cell by cell — yet each comes with its own
formats and tools. U-Chrom puts them in one data model, ChromData (cells › traces › spots on a
shared locus axis, with contact maps, RNA, chromatin marks and cell positions linked per cell), and
builds the analyses on it: import, 3-D reconstruction, structure calling, per-locus features,
single-cell embeddings, an interactive web browser and an open data atlas.
import uchrom as uc
import uchrom.datasets as ds
cd = ds.load("takei2021_mesc") # chromatin tracing (4DN FOF-CT), built once
tads = uc.tl.call_tads(cd, chrom="chr3") # TADs from 3-D distances
cd.write("takei2021.chromdata.zarr") # one store, read in parts later
python -m uchrom_browser takei2021.chromdata.zarr # look at it in the web browser
New here? Start with installation, the quick start and the concepts behind the data model.
By data type¶
Each chapter takes one kind of data from its files to a ChromData and through the analyses made for it,
step by step, with tutorials on real data.
Data |
Steps |
|---|---|
reading tracing data · from detections to traces · filling missing loci · calling structures: loops, TADs, domains, compartments |
|
contact maps per cell · 3-D structures of single cells · cell embeddings |
|
structures from a bulk map: MDS, IGM · Hi-C with imaging: GEM-FISH |
Common to all data¶
Chapter |
What it covers |
Package / module |
|---|---|---|
|
|
|
distance maps, variance features, signals and peaks along the genome, annotation |
|
|
the web browser, the data atlas, plots |
|