Repositories list

• utils

  Public
  various util modules shared amongst several projects in our organization

  Python

  •

  MIT License

  •1•4•1•8•Updated Feb 28, 2025Feb 28, 2025

• dcicwrangling

  Public
  Python

  •0•0•0•3•Updated Feb 25, 2025Feb 25, 2025

• Submit4DN

  Public
  Developing tools for data submission, curation and control

  Python

  •

  MIT License

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

• shared-portal-components

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

  JavaScript

  •

  MIT License

  •0•2•0•12•Updated Feb 20, 2025Feb 20, 2025

• snovault

  Public
  The SnoVault general purpose hybrid object-relational database

  Python

  •

  Other

  •1•1•0•13•Updated Feb 12, 2025Feb 12, 2025

• fourfront

  Public
  Data portal for submitting and viewing genomic data

  JavaScript

  •

  MIT License

  •2•13•0•31•Updated Feb 11, 2025Feb 11, 2025

• fish_omics_format

  Public
  0•1•3•2•Updated Feb 11, 2025Feb 11, 2025

• 4dn-cloud-infra

  Public
  Cloud Formation templates for 4dn-dcic AWS environments

  Python

  •0•0•0•5•Updated Feb 11, 2025Feb 11, 2025

• foursight

  Public
  Providing insight into your application using AWS infrastructure.

  Python

  •

  MIT License

  •0•7•0•2•Updated Jan 30, 2025Jan 30, 2025

• pairix

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

  pythoncbioinformatics+ 5pairshi-crandom-accessbgzippypairix

  C

  •

  MIT License

  •14•88•6•3•Updated Jan 28, 2025Jan 28, 2025

• foursight-core

  Public
  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+ 5coolerbwapairixjuicerpairsqc

  Common Workflow Language

  •

  MIT License

  •18•59•2•0•Updated Nov 26, 2024Nov 26, 2024

• 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+ 10snakemakeaws-lambdapipelinescondawdlcwlaws-step-function+ 3

  Python

  •

  MIT License

  •28•70•19•7•Updated Nov 21, 2024Nov 21, 2024

• Benchmark

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 20, 2024Nov 20, 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

  JavaScript

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

• jupyterhub-docker

  Public
  Python

  •0•0•0•0•Updated Sep 11, 2024Sep 11, 2024

• tibanna_ff

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

  Python

  •

  MIT License

  •0•3•0•1•Updated Sep 5, 2024Sep 5, 2024

• docker-4dn-RE-checker

  Public
  Perl

  •2•2•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

  •7•68•15•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

  •223•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

  •14•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

• snakemake-executor-plugin-tibanna

  Public
  A Snakemake executor plugin for Amazon AWS workflow exection with tibanna.

  Python

  •

  MIT License

  •1•0•1•1•Updated Dec 8, 2023Dec 8, 2023