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gunz-cm 2.28.1 documentation
gunz-cm 2.28.1 documentation

The Gunz Ecosystem

  • Gunz-ML (SDK)
  • Gunz-CM (Matrix)
  • Gunz-Utils (Core)

Getting Started

  • Getting Started with Gunz-CM
  • Installation
  • Quickstart
  • Core Concepts

User Guide

  • User Guide

Technical Reference

  • GZCM Format
  • gunz_cm
    • gunz_cm package
      • gunz_cm.cli
      • gunz_cm.compressions
        • gunz_cm.compressions.bsc_encoder
        • gunz_cm.compressions.bsc_decoder
        • gunz_cm.compressions.cmc_encoder
        • gunz_cm.compressions.cmc_decoder
        • gunz_cm.compressions.cmc_zstd_encoder
        • gunz_cm.compressions.cmc_zstd_decoder
        • gunz_cm.compressions.zstd_encoder
        • gunz_cm.compressions.zstd_decoder
      • gunz_cm.converters
      • gunz_cm.datasets
      • gunz_cm.io
      • gunz_cm.loaders
      • gunz_cm.metrics package
        • gunz_cm.metrics.reconstruction
        • gunz_cm.metrics.ren package
          • gunz_cm.metrics.ren.wrappers
      • gunz_cm.pipeline
      • gunz_cm.preprocs package
        • gunz_cm.preprocs.matrices
        • gunz_cm.preprocs.points
        • gunz_cm.preprocs.transforms
      • gunz_cm.reconstructions package
        • gunz_cm.reconstructions.objectives
        • gunz_cm.reconstructions.preprocs
        • gunz_cm.reconstructions.implementations
        • gunz_cm.reconstructions.utils
      • gunz_cm.resolution_enhancements package
        • gunz_cm.resolution_enhancements.datasets
        • gunz_cm.resolution_enhancements.preprocs
        • gunz_cm.resolution_enhancements.transforms
      • gunz_cm.samplers
      • gunz_cm.structs package
      • gunz_cm.utils
      • gunz_cm.visualizations
  • Tutorials
    • Tutorial: Load HIC contact matrix data
    • Tutorial: Load COOL / MCOOL contact matrix data
    • Tutorial: Convert contact matrices to alternate formats
    • Tutorial: Visualizing Hi-C contact matrices with gunz_cm.visualizations
    • Tutorial: Load a real Hi-C dataset via GUNZ_CM_TUTORIAL_DATAThis tutorial walks through loading the canonical public GM12878chr1 Hi-C dataset from 4DNucleome (accession 4DNFI1UEG1HD)using the gunz_cm.loaders API. The path to the file isresolved at runtime from the GUNZ_CM_TUTORIAL_DATA env var, sono contributor’s filesystem path is ever hardcoded.## SetupBefore running, populate the data directory once:bashmkdir -p ~/gunz_cm_tutorial_datapython scripts/download_tutorial_data.py --name gm12878_chr1_1mb \    --target ~/gunz_cm_tutorial_dataexport GUNZ_CM_TUTORIAL_DATA=~/gunz_cm_tutorial_data## Learning Objectives* Resolve a canonical dataset via notebooks/_tutorial_data.load_tutorial_dataset.* Load a .hic contact matrix at a specific resolution + chromosome.* Inspect metadata (resolutions, balancing, chromosome info).* Apply KR balancing and read the matrix back as COO.## Estimated TimeApproximately 5 minutes after the data is downloaded.## Prerequisites* gunz-cm installed (this repo).* GUNZ_CM_TUTORIAL_DATA set to a directory containing 4DNFI1UEG1HD.hic.
    • Tutorial: Load a real Micro-C dataset via GUNZ_CM_TUTORIAL_DATAThis tutorial walks through loading the canonical public mESCMicro-C chr19 dataset from 4DNucleome (accession4DNFI9GMP7J3) using the gunz_cm.loaders API.## Setupbashmkdir -p ~/gunz_cm_tutorial_datapython scripts/download_tutorial_data.py --name mESC_microc_chr19_50kb \    --target ~/gunz_cm_tutorial_dataexport GUNZ_CM_TUTORIAL_DATA=~/gunz_cm_tutorial_data## Learning Objectives* Resolve a multi-resolution .mcool file via the helper.* Inspect the available zoom levels (get_resolutions).* Load at the finest 50 kb resolution on chr19 with KR balancing.
    • Tutorial: Filter and balance a contact matrix
    • Tutorial: KR and ICE balancing for Hi-C contact matrices
    • Tutorial: Downsample a Hi-C contact matrix to a coarser resolution
    • Tutorial: Preprocessing Pipeline (matrices module)
    • Tutorial: 3D Structure Visualization
    • Tutorial: The Full Procrustes Surface
    • Tutorial: Reconstruction Performance Evaluators
    • Tutorial: Typed Data Shapes in gunz_cm.structs
    • Tutorial: PyTorch Dataset Zoo
    • Tutorial: Tutorial 25: GZCM Codec Registry and the v5.1 Wire-Format Contract
    • Tutorial: Tutorial 26: GZCM Codec Picker and Adaptive Codec Selection
    • Tutorial: Tutorial 27: Writing GZCM v4 Files with Adaptive Codec Picker
    • Tutorial: Tutorial 28: Reading GZCM v4 Files with the LRU Tile Cache
    • Tutorial: Tutorial 29: Using GzcmDataset with PyTorch DataLoader
    • Tutorial: Tutorial 30: Sparse-COO DataLoader with SparseCODataset.from_coo
    • Tutorial: Tutorial 31: End-to-End In-Memory Hi-C Pipeline (synth -> model)

Tutorials

  • Tutorials
    • Tutorial: Load HIC contact matrix data
    • Tutorial: Load COOL / MCOOL contact matrix data
    • Tutorial: Convert contact matrices to alternate formats
    • Tutorial: Visualizing Hi-C contact matrices with gunz_cm.visualizations
    • Tutorial: Load a real Hi-C dataset via GUNZ_CM_TUTORIAL_DATAThis tutorial walks through loading the canonical public GM12878chr1 Hi-C dataset from 4DNucleome (accession 4DNFI1UEG1HD)using the gunz_cm.loaders API. The path to the file isresolved at runtime from the GUNZ_CM_TUTORIAL_DATA env var, sono contributor’s filesystem path is ever hardcoded.## SetupBefore running, populate the data directory once:bashmkdir -p ~/gunz_cm_tutorial_datapython scripts/download_tutorial_data.py --name gm12878_chr1_1mb \    --target ~/gunz_cm_tutorial_dataexport GUNZ_CM_TUTORIAL_DATA=~/gunz_cm_tutorial_data## Learning Objectives* Resolve a canonical dataset via notebooks/_tutorial_data.load_tutorial_dataset.* Load a .hic contact matrix at a specific resolution + chromosome.* Inspect metadata (resolutions, balancing, chromosome info).* Apply KR balancing and read the matrix back as COO.## Estimated TimeApproximately 5 minutes after the data is downloaded.## Prerequisites* gunz-cm installed (this repo).* GUNZ_CM_TUTORIAL_DATA set to a directory containing 4DNFI1UEG1HD.hic.
    • Tutorial: Load a real Micro-C dataset via GUNZ_CM_TUTORIAL_DATAThis tutorial walks through loading the canonical public mESCMicro-C chr19 dataset from 4DNucleome (accession4DNFI9GMP7J3) using the gunz_cm.loaders API.## Setupbashmkdir -p ~/gunz_cm_tutorial_datapython scripts/download_tutorial_data.py --name mESC_microc_chr19_50kb \    --target ~/gunz_cm_tutorial_dataexport GUNZ_CM_TUTORIAL_DATA=~/gunz_cm_tutorial_data## Learning Objectives* Resolve a multi-resolution .mcool file via the helper.* Inspect the available zoom levels (get_resolutions).* Load at the finest 50 kb resolution on chr19 with KR balancing.
    • Tutorial: Filter and balance a contact matrix
    • Tutorial: KR and ICE balancing for Hi-C contact matrices
    • Tutorial: Downsample a Hi-C contact matrix to a coarser resolution
    • Tutorial: Preprocessing Pipeline (matrices module)
    • Tutorial: 3D Structure Visualization
    • Tutorial: The Full Procrustes Surface
    • Tutorial: Reconstruction Performance Evaluators
    • Tutorial: Typed Data Shapes in gunz_cm.structs
    • Tutorial: PyTorch Dataset Zoo
    • Tutorial: Tutorial 25: GZCM Codec Registry and the v5.1 Wire-Format Contract
    • Tutorial: Tutorial 26: GZCM Codec Picker and Adaptive Codec Selection
    • Tutorial: Tutorial 27: Writing GZCM v4 Files with Adaptive Codec Picker
    • Tutorial: Tutorial 28: Reading GZCM v4 Files with the LRU Tile Cache
    • Tutorial: Tutorial 29: Using GzcmDataset with PyTorch DataLoader
    • Tutorial: Tutorial 30: Sparse-COO DataLoader with SparseCODataset.from_coo
    • Tutorial: Tutorial 31: End-to-End In-Memory Hi-C Pipeline (synth -> model)
  • Tutorial: Load HIC contact matrix data
  • Tutorial: Load COOL / MCOOL contact matrix data
  • Tutorial: Convert contact matrices to alternate formats
  • Tutorial: Visualizing Hi-C contact matrices with gunz_cm.visualizations
  • Tutorial: Filter and balance a contact matrix
  • Tutorial: KR and ICE balancing for Hi-C contact matrices
  • Tutorial: Downsample a Hi-C contact matrix to a coarser resolution

Project Info

  • Changelog

Migration Guides

  • GZCM v3 → v4 migration guide
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gunz_cm.metrics package#

Subpackages#

  • gunz_cm.metrics.reconstruction
    • Module contents
  • gunz_cm.metrics.ren package
    • Subpackages
      • gunz_cm.metrics.ren.wrappers
        • Module contents
    • Module contents

Module contents#

Module init.

Examples

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