uchrom.tl / uchrom.pp¶
Flat, scanpy-style aliases over the domain modules.
uchrom.tl — flat, scanpy-style aliases for analysis tools.
Tools add annotations (structures, features, embeddings) to a
ChromData. The implementations live in the domain modules
(uchrom.strc, uchrom.fea, …); these aliases only dispatch on
method= and forward every other keyword unchanged, so they follow the
same calling convention (chrom=None, params=, key_added=,
copy=):
import uchrom as uc
uc.tl.call_tads(cd, method="arcfish") # strc.tad.call_tads_by_pval
uc.tl.call_loops(cd) # strc.loop.call_loops_axiswise_f
uc.tl.call_compartments(cd) # strc.comp.call_compartments_axes_pc
uc.tl.reconstruct_sc("cell.pairs") # recon.sc.reconstruct_ember (EMber)
- uchrom.tl.call_compartments(cd, *, method: str = 'axes_pc', **kwargs)[source]¶
Call A/B compartments.
method:"axes_pc"→uchrom.strc.comp.call_compartments_axes_pc().
- uchrom.tl.call_loops(cd, *, method: str = 'axiswise_f', **kwargs)[source]¶
Call loops.
method:"axiswise_f"→uchrom.strc.loop.call_loops_axiswise_f().
- uchrom.tl.call_tads(cd, *, method: str = 'arcfish', **kwargs)[source]¶
Call TADs / domains.
method:"arcfish"(alias"pval") →uchrom.strc.tad.call_tads_by_pval();"fishnet"→uchrom.strc.tad.call_domains_fishnet();"di"→uchrom.strc.tad.call_tads_di()(linked Hi-C contacts).
- uchrom.tl.reconstruct_sc(contacts, *, method: str = 'ember', **kwargs)[source]¶
Single-cell Hi-C 3-D reconstruction -> new
ChromData.method:"ember"->uchrom.recon.sc.reconstruct_ember();"nucdyn"->uchrom.recon.sc.reconstruct_nucdyn().
uchrom.pp — flat, scanpy-style aliases for preprocessing.
Preprocessing changes coordinates / spots (impute, align, normalise, rebin). The implementations live in the domain modules; these aliases forward to them:
import uchrom as uc
cd_imputed = uc.pp.impute(cd, method="snapfish") # im.impute.impute_coordinates