24 projects
dcicutils
Utility package for interacting with the 4DN Data Portal and other 4DN resources
foursight
Serverless Chalice Application for Monitoring
foursight-cgap
Serverless Chalice Application for Monitoring
foursight-core
Serverless Chalice Application for Monitoring
smaht-submitr
Support for uploading file submissions to SMAHT.
foursight-smaht
Serverless Chalice Application for Monitoring
submit4dn
Utility package for submitting data to the 4DN Data Portal
tibanna-ff
Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud.
magma-suite
Collection of tools to manage meta-workflows automation.
dcicsnovault
Storage support for 4DN Data Portals.
encoded-core
Core data models for Park Lab ENCODE based projects
tibanna
Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud.
submit-cgap
Support for uploading file submissions to the Clinical Genomics Analysis Platform (CGAP).
hic2cool
Converter between hic files (from juicer) and single-resolution or multi-resolution cool files (for cooler). Both hic and cool files describe Hi-C contact matrices. Intended to be lightweight, this can be used as an imported package or a stand-alone Python tool for command line conversion.
dcicwrangling
Scripts and Jupyter notebooks for 4DN wrangling
portal-pipeline-utils
Utilities for deploying pipelines and interfacing with portal infrastructure.
dcicpyvcf
Variant Call Format (VCF) parser for Python
benchmark-4dn
Benchmark functions that returns total space, mem, cpu given input size and parameters for the CWL workflows
cgap-pipeline-utils
Collection of utilities for cgap-pipeline
granite-suite
granite is a collection of software to call, filter and work with genomic variants.
subprocess-middleware-c4
Subprocess WSGI middleware and Pyramid tween.
bamsnap-cgap
A converter from .bam to .png for specific genomic region.
python-lambda-4dn
A forked version of python-lambda for 4DN-DCIC use in packaging and deploying lambda functions.
pypairix
Pypairix is a Python module for fast querying on a pairix-indexed bgzipped text file that contains a pair of genomic coordinates per line. For more information, see: https://github.com/4dn-dcic/pairix/blob/master/README.md.
