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@aidenlab

Aiden Lab

The Center for Genome Architecture

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  1. juicer juicer Public

    A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

    Shell 475 194

  2. Juicebox Juicebox Public

    Visualization and analysis software for Hi-C data -

    Java 285 61

  3. 3d-dna 3d-dna Public

    3D de novo assembly (3D DNA) pipeline

    Shell 223 58

  4. straw straw Public

    Extract data quickly from Juicebox via straw

    C++ 69 35

  5. BEAR BEAR Public

    BEAR: viral diagnostic analysis pipeline for SARS-CoV-2

    Shell 6 1

  6. EigenVector EigenVector Public

    Forked from moshe-olshansky/EigenVector

    R functions for very fast eigenvector calculation

    C 11 4

Repositories

Showing 10 of 38 repositories
  • hic-straw Public

    Command line and web utilities for reading .hic contact matrix files

    aidenlab/hic-straw’s past year of commit activity
    JavaScript 10 MIT 4 0 1 Updated Feb 26, 2026
  • swtool Public

    Convert legacy Spacewalk file (.swt) to modern HDF5 based binary format (.sw)

    aidenlab/swtool’s past year of commit activity
    JavaScript 0 0 0 0 Updated Feb 26, 2026
  • spacewalk Public
    aidenlab/spacewalk’s past year of commit activity
    JavaScript 0 MIT 0 0 0 Updated Feb 25, 2026
  • juicebox.js Public

    HiC contact matrix visualization

    aidenlab/juicebox.js’s past year of commit activity
    JavaScript 22 MIT 15 22 1 Updated Feb 25, 2026
  • juicebox-web Public
    aidenlab/juicebox-web’s past year of commit activity
    JavaScript 3 1 3 0 Updated Feb 22, 2026
  • juicebox-mcp Public

    MCP-enabled version of juicebox.js - HiC contact matrix visualization

    aidenlab/juicebox-mcp’s past year of commit activity
    JavaScript 0 MIT 1 0 0 Updated Jan 6, 2026
  • hello3dmcp-server Public

    MCP server for controlling 3D model visualization via Model Context Protocol

    aidenlab/hello3dmcp-server’s past year of commit activity
    JavaScript 0 0 0 0 Updated Dec 30, 2025
  • hello3dmcp-frontend Public

    3D interactive model visualization built with Three.js, connects to MCP server via WebSocket

    aidenlab/hello3dmcp-frontend’s past year of commit activity
    JavaScript 0 0 0 0 Updated Dec 22, 2025
  • Hello3DLLM Public

    Exploration of LLM Enabled Interactive Visual Apps

    aidenlab/Hello3DLLM’s past year of commit activity
    JavaScript 0 0 0 0 Updated Nov 29, 2025
  • juicer Public

    A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

    aidenlab/juicer’s past year of commit activity
    Shell 475 MIT 194 106 9 Updated Aug 31, 2025
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