Repositories list

• juicebox.js

  Public
  HiC contact matrix visualization

  JavaScript

  •

  MIT License

  •1616 forks•2424 stars•1414 issues•00 pull requests•Updated Sep 23, 2026Sep 23, 2026

• juicebox-web

  Public
  JavaScript

  •11 fork•33 stars•55 issues•00 pull requests•Updated Sep 17, 2026Sep 17, 2026

• spacewalk

  Public
  JavaScript

  •

  MIT License

  •00 forks•00 stars•11 issue•00 pull requests•Updated Sep 17, 2026Sep 17, 2026

• juicer

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

  bioinformaticsgenomicsngs+ 3

  bioinformaticsgenomicsngshi-c3d-genome3d-genome-browser

  Shell

  •

  MIT License

  •192192 forks•490490 stars•108108 issues•1010 pull requests•Updated Sep 15, 2026Sep 15, 2026

• hic-straw

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

  JavaScript

  •

  MIT License

  •55 forks•1010 stars•22 issues•11 pull request•Updated Sep 10, 2026Sep 10, 2026

• microsoft-skills

  Public
  Skills, MCP servers, Custom Agents, Agents.md for SDKs to ground Coding Agents

  TypeScript

  •

  MIT License

  •351351 forks•00 stars•00 issues•00 pull requests•Updated Sep 6, 2026Sep 6, 2026

• Juicebox

  Public
  Visualization and analysis software for Hi-C data -

  Java

  •

  MIT License

  •6161 forks•304304 stars•265265 issues•33 pull requests•Updated Sep 2, 2026Sep 2, 2026

• spacewalk-fixtures

  Public archive
  Demo ensemble .sw fixtures for the Spacewalk app's Load From List, served via jsDelivr CDN

  00 forks•00 stars•00 issues•00 pull requests•Updated Jun 4, 2026Jun 4, 2026

• hdf5-indexed-reader

  Public
  Module based on jsfive for efficient remote access of very large HDF5 files

  JavaScript

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 15, 2026May 15, 2026

• swtool

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

  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 30, 2026Apr 30, 2026

• pc2bs

  Public
  Point-cloud Spacewalk .sw to ball-and-stick (CLI, one-way)

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 22, 2026Apr 22, 2026

• juicebox-mcp

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

  JavaScript

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jan 6, 2026Jan 6, 2026

• hello3dmcp-server

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

  JavaScript

  •11 fork•11 star•00 issues•00 pull requests•Updated Dec 30, 2025Dec 30, 2025

• hello3dmcp-frontend

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

  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 22, 2025Dec 22, 2025

• Hello3DLLM

  Public
  Exploration of LLM Enabled Interactive Visual Apps

  JavaScript

  •00 forks•11 star•00 issues•00 pull requests•Updated Nov 29, 2025Nov 29, 2025

• straw

  Public
  Extract data quickly from Juicebox via straw

  C++

  •

  MIT License

  •3535 forks•7070 stars•3131 issues•11 pull request•Updated Apr 6, 2025Apr 6, 2025

• juicebox.js_AL

  Public
  HiC contact matrix visualization

  JavaScript

  •

  MIT License

  •1616 forks•00 stars•00 issues•00 pull requests•Updated Feb 15, 2025Feb 15, 2025

• sw2stl

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 2, 2024Aug 2, 2024

• 3d-carta

  Public
  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 22, 2024May 22, 2024

• clear-tools

  Public
  Chromatin Landscape Exploration, Analysis, and Research Tools

  Java

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Apr 26, 2024Apr 26, 2024

• 3d-dna

  Public
  3D de novo assembly (3D DNA) pipeline

  Shell

  •

  MIT License

  •5959 forks•229229 stars•6666 issues•11 pull request•Updated Nov 29, 2023Nov 29, 2023

• BEAR

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

  bioinformaticsviral-metagenomicscovid-19

  bioinformaticsviral-metagenomicscovid-19

  Shell

  •

  MIT License

  •11 fork•66 stars•11 issue•00 pull requests•Updated Feb 23, 2023Feb 23, 2023

• PAP

  Public
  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 23, 2023Jan 23, 2023

• EigenVector

  Public
  R functions for very fast eigenvector calculation

  C

  •99 forks•1111 stars•00 issues•11 pull request•Updated Jan 18, 2023Jan 18, 2023

• HiCTools

  Public
  Java

  •

  MIT License

  •33 forks•1212 stars•11 issue•00 pull requests•Updated Jan 18, 2023Jan 18, 2023

• welcome

  Public
  Getting started with Hi-C data analysis

  HTML

  •

  MIT License

  •00 forks•66 stars•00 issues•00 pull requests•Updated Dec 4, 2022Dec 4, 2022

• welcome-images

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Dec 4, 2022Dec 4, 2022

• mmba

  Public
  Moshe's matrix balancing algorithm

  C

  •00 forks•00 stars•11 issue•00 pull requests•Updated Oct 12, 2022Oct 12, 2022

• java-straw

  Public
  Java

  •

  MIT License

  •44 forks•00 stars•00 issues•00 pull requests•Updated Sep 29, 2022Sep 29, 2022

• JuiceboxGUI

  Public
  Java

  •

  MIT License

  •22 forks•88 stars•33 issues•00 pull requests•Updated Sep 29, 2022Sep 29, 2022