Explore @4dn-dcic Open Source projects

4D Nucleome Data Coordination and Integration Center (@4dn-dcic)

4dn-dcic

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384
Global Org. Rank 27,738 (Top 9 %)
Registered over 7 years ago
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Python
40.0 %

Shell
28.6 %

Common Workflow Language 8.6 %

JavaScript
8.6 %

C
5.7 %

Dockerfile
2.9 %

Perl
2.9 %

HTML
2.9 %
Location 🇺🇸 United States
Country Total Rank 18,690
Country Ranking

Common Workflow Language 2

C
2,210

Dockerfile
3,371

Perl
3,668

Python
6,229

Shell
6,390

HTML
8,521

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

Common Workflow Language

fourfront

Data portal for submitting and viewing genomic data

pairsqc

QC report generator for Hi-C pairs file

react-workflow-viz

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

pipelines-cwl

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

Common Workflow Language

Rpairix

R binder for pairix - 2D/1D genomic indexing and querying on bgzipped text file

foursight

Providing insight into your application using AWS infrastructure.

4dn-policies

Policies for the NIH Common Fund 4D Nucleome Network.

Submit4DN

Developing tools for data submission, curation and control

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

utils

various util modules shared amongst several projects in our organization

tibanna_ff

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

docker-md5

shared-portal-components

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

bam2pairs

GiniQC

Tool for single-cell Hi-C quality control

docker_templates

foursight-core

docker-4dn-cut-and-run-pipeline

CUT&RUN Pipeline

docker-sort-bam

docker-bwa-mem

snovault

The SnoVault general purpose hybrid object-relational database

docker-bam2pairs

docker-dedup-hic

docker-4dn-repliseq

Docker for 4DN Repli-seq processing pipeline

Common Workflow Language

docker-sha256

hicfilters

docker-4dn-insulator-score-caller

docker-hicfilters

simple-s3fs

A simple (read-only) FUSE-based file system for S3 buckets.

mochee

docker-4dn-compartments-caller

docker-4dn-RE-checker

docker-merge-pairs

docker-4dn-mergebed

Docker/CWL for a 4DN util workflow for merging and sorting gzipped bed files