All

94 repositories

utils
Public
various util modules shared amongst several projects in our organization
u01ca200059 ot2od032119
u01ca200059 ot2od032119
Python
•
MIT License
•1•4•1•10•Updated Jun 17, 2026Jun 17, 2026
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 proces…
docker aws bioinformatics
docker aws bioinformatics snakemake aws-lambda pipelines conda wdl cwl aws-step-function
Python
•
MIT License
•28•72•19•8•Updated Jun 17, 2026Jun 17, 2026
foursight-core
Public
u01ca200059 ot2od032119
u01ca200059 ot2od032119
Python
•
MIT License
•0•0•0•1•Updated Jun 17, 2026Jun 17, 2026
snovault
Public
The SnoVault general purpose hybrid object-relational database
Python
•
Other
•1•1•0•10•Updated Jun 17, 2026Jun 17, 2026
shared-portal-components
Public
Common components for use by 4DN and CGAP portal(s)
u01ca200059 ot2od032119
u01ca200059 ot2od032119
JavaScript
•
MIT License
•0•2•0•13•Updated Jun 9, 2026Jun 9, 2026
react-workflow-viz
Public
React component for visualizing CWL-like workflows (and similar data)
visualization workflow provenance
visualization workflow provenance u01ca200059 ot2od032119
JavaScript
•0•11•2•13•Updated Jun 2, 2026Jun 2, 2026
foursight
Public
Providing insight into your application using AWS infrastructure.
u01ca200059 ot2od032119
u01ca200059 ot2od032119
Python
•
MIT License
•0•7•0•4•Updated May 21, 2026May 21, 2026
fish_omics_format
Public
u01ca200059 ot2od032119
u01ca200059 ot2od032119
0•3•3•0•Updated May 12, 2026May 12, 2026
4dn-cloud-infra
Public
Cloud Formation templates for 4dn-dcic AWS environments
u01ca200059 ot2od032119
u01ca200059 ot2od032119
Python
•0•0•0•7•Updated Apr 30, 2026Apr 30, 2026
python-lambda
Public
A toolkit for developing and deploying serverless Python code in AWS Lambda.
Python
•
Other
•1•0•0•2•Updated Apr 13, 2026Apr 13, 2026
snakemake-executor-plugin-tibanna
Public
A Snakemake executor plugin for Amazon AWS workflow exection with tibanna.
Python
•
MIT License
•1•0•1•1•Updated Apr 7, 2026Apr 7, 2026
tibanna_ff
Public
This is an extension of Tibanna that integrates with 4DN/CGAP/SMaHT data portals.
u01ca200059 ot2od032119
u01ca200059 ot2od032119
Python
•
MIT License
•0•3•0•3•Updated Apr 3, 2026Apr 3, 2026
fourfront
Public
Data portal for submitting and viewing genomic data
u01ca200059 ot2od032119
u01ca200059 ot2od032119
JavaScript
•
MIT License
•2•14•0•31•Updated Mar 5, 2026Mar 5, 2026
open-data-registry
Public
A registry of publicly available datasets on AWS
Python
•
Apache License 2.0
•1.2k•0•0•0•Updated Dec 26, 2025Dec 26, 2025
Benchmark
Public
Python
•
MIT License
•0•0•0•0•Updated Sep 5, 2025Sep 5, 2025
dcicwrangling
Public
Python
•0•0•0•3•Updated Aug 25, 2025Aug 25, 2025
spt_format
Public
4DN Single Particle Tracking (SPT) format
0•0•0•1•Updated Jul 1, 2025Jul 1, 2025
jupyterhub-docker
Public
u01ca200059 ot2od032119
u01ca200059 ot2od032119
Python
•0•0•0•0•Updated Apr 17, 2025Apr 17, 2025
Submit4DN
Public
Developing tools for data submission, curation and control
u01ca200059 ot2od032119
u01ca200059 ot2od032119
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
python c bioinformatics
python c bioinformatics pairs hi-c random-access bgzip pypairix u01ca200059 ot2od032119
C
•
MIT License
•15•92•8•3•Updated Jan 28, 2025Jan 28, 2025
docker-4dn-hic
Public
Docker for 4DN Hi-C processing pipeline
docker bioinformatics hi-c
docker bioinformatics hi-c cooler bwa pairix juicer pairsqc u01ca200059 ot2od032119
Common Workflow Language
•
MIT License
•16•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
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.
converter bioinformatics hi-c
converter bioinformatics hi-c cooler juicer contact-matrices
Python
•
MIT License
•10•74•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
sbg pipeline cwl
sbg pipeline cwl tibanna
Common Workflow Language
•
MIT License
•5•10•0•1•Updated Jul 11, 2024Jul 11, 2024
PyVCF
Public
A Variant Call Format reader for Python.
Python
•
Other
•224•0•0•1•Updated Jul 3, 2024Jul 3, 2024

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4D Nucleome Data Coordination and Integration Center

All

All

94 repositories

utils

tibanna

foursight-core

snovault

shared-portal-components

react-workflow-viz

foursight

fish_omics_format

4dn-cloud-infra

python-lambda

snakemake-executor-plugin-tibanna

tibanna_ff

fourfront

open-data-registry

Benchmark

dcicwrangling

spt_format

jupyterhub-docker

Submit4DN

pairix

docker-4dn-hic

docker-4dn-bedtobeddb

docker-md5

docker-4dn-RE-checker

docker-4dn-mcoolQC

hic2cool

docker-fastqc

docker-4dn-fastq-first-line

pipelines-cwl

PyVCF

All

All

Repositories list

94 repositories