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U-Chrom 0.3 (dev)
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U-Chrom 0.3 (dev)

Getting started

  • Installation
  • Quick start
  • Concepts
  • Datasets

By data type

  • Chromatin tracing
    • Importing FOF-CT chromatin-tracing data
    • Importing PyHiM chromatin-trace tables (ECSV)
    • Spot-to-trace alignment with jie
    • Imputing missing FISH coordinates
    • The 4DN FISH Omics Format (FOF-CT)
    • From detections to traces: the jie aligner
  • Imaging multi-omics: DNA seqFISH+
    • Importing seqFISH+ multi-omics data (Takei 2025 cerebellum)
  • Single-cell and spatial Hi-C
    • Single-cell 3-D genome reconstruction: NucDynamics and EMber
    • Contact-map cell embedding with FastHigashi
    • Single-cell reconstruction: methods and parameters
  • Bulk Hi-C
    • Bulk Hi-C to 3-D: MDS and IGM population deconvolution
    • Joint Hi-C + FISH reconstruction with GEM-FISH
    • Bulk Hi-C: methods

Common to all data

  • Data model & storage
    • ChromData: the data model
    • The .chromdata.zarr store
    • ChromData
    • Linked Multi-Omics
  • Structure calling
    • Loop calling on chromatin tracing data
    • TAD calling
    • Single-allele domains with FISHnet
    • A/B compartments from chromatin tracing
    • Structure identification
  • Per-locus features
    • Per-locus features
  • Cells & embeddings
    • Cell embeddings and clusters across modalities
    • Contact-map cell embedding with FastHigashi
  • Visualisation
    • Visualisation: plots and the web browser
    • The web browser
    • The data atlas

Reference

  • API reference
    • chromdata (the data model)
    • uchrom.tl / uchrom.pp
    • uchrom.io
    • uchrom.im
    • uchrom.recon
    • uchrom.recon.fish
    • uchrom.strc.loop
    • uchrom.strc.tad
    • uchrom.strc.comp
    • uchrom.strc.enrichment
    • uchrom.fea
    • uchrom.emb
    • uchrom.pl
    • uchrom.utils
    • uchrom_browser (the web browser)
  • File formats
  • ChromData Specification
  • Datasets: sources and recipes
  • ChromData 2.0 Design
  • Development
  • Changelog
  • License
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