Repositories list

• fourfront

  Public
  Data portal for submitting and viewing genomic data

  u01ca200059ot2od032119

  JavaScript

  •

  MIT License

  •2•14•0•31•Updated Jul 29, 2025Jul 29, 2025

• foursight

  Public
  Providing insight into your application using AWS infrastructure.

  u01ca200059ot2od032119

  Python

  •

  MIT License

  •0•7•0•2•Updated Jul 29, 2025Jul 29, 2025

• snovault

  Public
  The SnoVault general purpose hybrid object-relational database

  u01ca200059ot2od032119

  Python

  •

  Other

  •1•1•0•11•Updated Jul 22, 2025Jul 22, 2025

• spt_format

  Public
  4DN Single Particle Tracking (SPT) format

  0•0•0•1•Updated Jul 1, 2025Jul 1, 2025

• 4dn-cloud-infra

  Public
  Cloud Formation templates for 4dn-dcic AWS environments

  u01ca200059ot2od032119

  Python

  •0•0•0•6•Updated Jun 30, 2025Jun 30, 2025

• dcicwrangling

  Public
  Python

  •0•0•0•3•Updated May 22, 2025May 22, 2025

• tibanna_ff

  Public
  This is an extension of Tibanna that integrates with 4DN/CGAP/SMaHT data portals.

  u01ca200059ot2od032119

  Python

  •

  MIT License

  •0•3•0•1•Updated May 20, 2025May 20, 2025

• fish_omics_format

  Public
  u01ca200059ot2od032119

  0•1•3•0•Updated Apr 28, 2025Apr 28, 2025

• jupyterhub-docker

  Public
  u01ca200059ot2od032119

  Python

  •0•0•0•0•Updated Apr 17, 2025Apr 17, 2025

• Benchmark

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 15, 2025Apr 15, 2025

• tibanna

  Public
  Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

  dockerawsbioinformatics+ 12snakemakeaws-lambdapipelinescondawdlcwlaws-step-function+ 5

  Python

  •

  MIT License

  •27•69•20•7•Updated Apr 11, 2025Apr 11, 2025

• shared-portal-components

  Public
  Common components for use by 4DN and CGAP portal(s)

  u01ca200059ot2od032119

  JavaScript

  •

  MIT License

  •0•2•0•12•Updated Mar 25, 2025Mar 25, 2025

• utils

  Public
  various util modules shared amongst several projects in our organization

  u01ca200059ot2od032119

  Python

  •

  MIT License

  •1•4•1•8•Updated Mar 21, 2025Mar 21, 2025

• Submit4DN

  Public
  Developing tools for data submission, curation and control

  u01ca200059ot2od032119

  Python

  •

  MIT License

  •0•4•1•1•Updated Feb 25, 2025Feb 25, 2025

• pairix

  Public
  1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

  pythoncbioinformatics+ 7pairshi-crandom-accessbgzippypairixu01ca200059ot2od032119

  C

  •

  MIT License

  •15•89•7•3•Updated Jan 28, 2025Jan 28, 2025

• foursight-core

  Public
  u01ca200059ot2od032119

  Python

  •

  MIT License

  •0•1•0•0•Updated Jan 10, 2025Jan 10, 2025

• docker-4dn-hic

  Public
  Docker for 4DN Hi-C processing pipeline

  dockerbioinformaticshi-c+ 7coolerbwapairixjuicerpairsqcu01ca200059ot2od032119

  Common Workflow Language

  •

  MIT License

  •17•61•4•0•Updated Nov 26, 2024Nov 26, 2024

• docker-4dn-bedtobeddb

  Public
  Shell

  •0•0•0•2•Updated Nov 14, 2024Nov 14, 2024

• docker-md5

  Public
  Shell

  •0•1•0•0•Updated Nov 12, 2024Nov 12, 2024

• react-workflow-viz

  Public
  React component for visualizing CWL-like workflows (and similar data)

  visualizationworkflowprovenance+ 2u01ca200059ot2od032119

  JavaScript

  •0•9•2•13•Updated Oct 30, 2024Oct 30, 2024

• docker-4dn-RE-checker

  Public
  Perl

  •1•4•0•1•Updated Jul 22, 2024Jul 22, 2024

• docker-4dn-mcoolQC

  Public
  Python

  •0•0•0•0•Updated Jul 22, 2024Jul 22, 2024

• hic2cool

  Public
  Lightweight converter between hic and cool contact matrices.

  bioinformaticshi-ccooler+ 3juicerconvertercontact-matrices

  Python

  •

  MIT License

  •10•73•16•5•Updated Jul 15, 2024Jul 15, 2024

• docker-fastqc

  Public
  Common Workflow Language

  •0•0•0•0•Updated Jul 12, 2024Jul 12, 2024

• docker-4dn-fastq-first-line

  Public
  Dockerfile

  •0•0•0•0•Updated Jul 11, 2024Jul 11, 2024

• pipelines-cwl

  Public
  Pipelines developed and used by 4DN-DCIC in Common Workflow Language

  cwltibannasbg+ 1pipeline

  Common Workflow Language

  •

  MIT License

  •5•9•0•1•Updated Jul 11, 2024Jul 11, 2024

• PyVCF

  Public
  A Variant Call Format reader for Python.

  Python

  •

  Other

  •225•0•0•1•Updated Jul 3, 2024Jul 3, 2024

• docker-4dn-bedtomultivec

  Public
  Shell

  •0•0•0•0•Updated Jun 14, 2024Jun 14, 2024

• higlass-docker

  Public
  Builds a docker container wrapping higlass-server and higlass-client in nginx

  Shell

  •

  MIT License

  •15•0•0•0•Updated Jun 12, 2024Jun 12, 2024

• post-deploy-perf-tests

  Public
  A collection of performance testing

  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 1, 2024Apr 1, 2024