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 — or browse every tutorial in the gallery.
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 |
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contact maps per cell · pseudo-bulk maps · 3-D structures of single cells · cell embeddings |
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calling structures from a map: compartments, domains, loops, pileups · 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 |
|
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the web browser, the data atlas, plots |
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