Shared Python utilities that help with interacting with Terra, TDR, BigQuery, and GCP to name a few.

This repo is for the metadata schemas associated with the HCA

Tutorials, workflows, and convenience scripts for Single Cell Portal

Helm charts for the Monster team in DSP

Awesome Docker Compose samples

An orchestration platform for the development, production, and observation of data assets.

A utility to validate a staging area before it is imported.

Clients for Python, R, javascript that interact with [terra, gen3, galaxy, others]

Hub for the Monster team in DSP Data Engineering

The next version of bwa-mem

Salmon Alevin (single cell) quantification wrapper module for GenePattern.

Salmon quantification wrapper module for GenePattern.

Design related materials for Project Jupyter

A GenePattern module for running the ssGSEA method

Neural bag of words code search implementation using PyTorch and data from the CodeSearchNet project.

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

GenePattern Module Development tools -- helper scripts for packaging and publishing modules

A GenePattern module for running the GSEA method

GenePattern Notebook Website (old)

Java implementation of RIGER and other gene enrichment methods, useful for RNAi and CRISPR screen analysis.

The GenePattern Server web application

Merges individial files containing HTSeq read counts into one file

Testing framework for GenePattern modules

Platform for integrating genomic analysis with Jupyter Notebooks.