4D Nucleome Data Coordination and Integration Center

pairix

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

tibanna

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.

hic2cool

Lightweight converter between hic and cool contact matrices.

docker-4dn-hic

Docker for 4DN Hi-C processing pipeline

fourfront

Data portal for submitting and viewing genomic data

react-workflow-viz

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

foursight

Providing insight into your application using AWS infrastructure.

docker-4dn-insulation-scores-and-boundaries-caller

Submit4DN

Developing tools for data submission, curation and control

utils

various util modules shared amongst several projects in our organization

shared-portal-components

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

tibanna_ff

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

repli-seq-pipeline

Scripts for the High-throughput Analysis of Replication Timing

chip-seq-pipeline2

4DN chip-seq pipeline, inherited from ENCODE chip-seq pipeline

docker-4dn-repliseq

Docker for 4DN Repli-seq processing pipeline

foursight-core

snovault

The SnoVault general purpose hybrid object-relational database

dcicwrangling

.github

Benchmark

brig

Conceptually, an offspring of Torb, but following a different path.

fish_omics_format

fourfront-governance

Governance, legal and policy information related to Fourfront

higlass-docker

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

jupyterhub-docker

post-deploy-perf-tests

A collection of performance testing

python-lambda

A toolkit for developing and deploying serverless Python code in AWS Lambda.

PyVCF

A Variant Call Format reader for Python.

snakemake-executor-plugin-tibanna

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

torb

Torbjörn our builder bot that builds our app and handles deployment