License

U-Chrom is released under the MIT license. See LICENSE in the repo for the full text.

Third-party code

  • uchrom.strc.loop, uchrom.fea.arc, uchrom.utils.stats implement algorithms described in Yu et al. 2025 (ArcFISH, bioRxiv 2025.11.26.690837). The implementation is independent of the upstream ArcFISH source (GPL-3.0).

  • The native NucDynamics engine (native/nucdyn, package u-chrom-nucdyn, used by uchrom.recon.sc.nucdyn) is a clean Rust re-implementation of NucDynamics (Stevens et al. 2017, Nature 544:59; tjs23/nuc_dynamics, LGPL-3.0) and is itself distributed under the LGPL-3.0-or-later as a separate package; uchrom only imports it.

  • The deprecated Taichi code in uchrom.recon.sc.nucdyn.nucdyn and uchrom.recon.sc.gem are Taichi reimplementations of the Nuc Dynamics and GEM algorithms published by the original authors.