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U-Chrom 0.2.0
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U-Chrom 0.2.0

Getting started

  • Installation
  • Concepts
  • Example data

Tutorials — Core & I/O

  • ChromData — the core data container
  • Importing FOF-CT imaging data
  • Importing PyHiM chromatin trace tables
  • Takei 2025 cerebellum — ChromData walkthrough + paper reproductions
  • Takei 2025 auto-discovery example

Tutorials — Reconstruction (recon)

  • 3D reconstruction from Hi-C data
  • GEM-FISH — joint Hi-C + FISH 3-D reconstruction

Tutorials — Imaging & tracing (im)

  • Spot-to-fiber tracing with jie on seqFISH+ data

Tutorials — Structure identification (strc)

  • Loop calling on tracing data
  • TAD calling
  • Single-cell domain calling with FISHnet
  • A/B compartment calling

Tutorials — Embedding (emb)

  • FastHigashi cell embedding

User guide

  • ChromData
  • I/O and file formats
  • Imaging & tracing (uchrom.im)
  • 3D reconstruction
  • Structure identification
  • Multi-omics Auto-discovery
  • Interactive 3D browser

API reference

  • API reference
    • uchrom.core
    • uchrom.auto_discovery
    • uchrom.io
    • uchrom.im
    • uchrom.recon
    • uchrom.recon.fish
    • uchrom.strc.loop
    • uchrom.strc.tad
    • uchrom.strc.comp
    • uchrom.fea
    • uchrom.pl
    • uchrom.utils
    • uchrom.browser

Project

  • Changelog
  • License
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API reference¶

Public modules, generated from source docstrings.

  • uchrom.core
  • uchrom.auto_discovery
  • uchrom.io
  • uchrom.im
  • uchrom.recon
  • uchrom.recon.fish
  • uchrom.strc.loop
  • uchrom.strc.tad
  • uchrom.strc.comp
  • uchrom.fea
  • uchrom.pl
  • uchrom.utils
  • uchrom.browser
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