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    30 repositories

    • aws-object-search

      Public
      Python
      •0•2•1•0•Updated Oct 27, 2025Oct 27, 2025

    • submissions-infrastructure

      Public
      Code to generate on-prem code infrastructure for the Submissions team at BCM-HGSC using conda
      Python
      •
      MIT License
      •1•0•15•0•Updated Oct 10, 2025Oct 10, 2025

    • SMaHT_MIMS

      Public
      Somatic Mosaicism across Human Tissues SV Benchmark
      Jupyter Notebook
      •1•2•0•0•Updated Oct 8, 2025Oct 8, 2025

    • liftover-helper

      Public
      Color liftover helper files for preprocessing
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 6, 2025Oct 6, 2025

    • aws-sso-workstations

      Public
      Secure EC2 workstation provisioning with AWS SSO authentication, ABAC permissions, and Session Manager access. Zero SSH, zero inbound ports.
      awssecurityec2ssoinfrastructure-as-codeworkstationssession-managerabacimage-builderiam-identity-center
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • request-tracker-tools

      Public
      CLI tools and package to help with automating Request Tracker using its REST 1.0 API
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 21, 2025Aug 21, 2025

    • GREGoR_AnVIL_automation

      Public
      submissions GREGoR AnVIL workflow
      Python
      •
      MIT License
      •0•0•7•0•Updated Jul 2, 2025Jul 2, 2025

    • s3-catapult

      Public
      Automated delivery of data batches from local filesystems to S3
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 26, 2025Jun 26, 2025

    • pm-utils

      Public
      Utilities for project managers
      Python
      •
      MIT License
      •0•0•7•0•Updated Jun 17, 2024Jun 17, 2024

    • qdpi

      Public
      Quick Delta and PIleups
      Rust
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated May 23, 2024May 23, 2024

    • gift-wrap

      Public
      A collection of wrappers used by the Submissions team
      Python
      •0•0•6•0•Updated Mar 19, 2024Mar 19, 2024

    • MFTS-Cleanup

      Public
      MFTS automatic emails and directory cleanup
      Python
      •
      MIT License
      •0•0•2•1•Updated Feb 23, 2024Feb 23, 2024

    • PGx4Statins-AI-Assistant

      Public
      AI assistant to answer patient and healthcare provider questions related to pharmacogenetic testing and results.
      Python
      •
      GNU General Public License v3.0
      •2•4•0•0•Updated Feb 12, 2024Feb 12, 2024

    • rdbms2s3

      Public
      This application imports data from RDBMS to AWS S3 bucket as CSV/parquet.
      Python
      •
      MIT License
      •0•0•2•0•Updated Dec 27, 2023Dec 27, 2023

    • TopMedSVQC

      Public
      TopMed SV QC scripts
      Jupyter Notebook
      •0•1•0•0•Updated Jun 24, 2023Jun 24, 2023

    • PGx-sico1b1-chatbot

      Public
      This is a demo project
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 12, 2023Jun 12, 2023

    • goatherd-scan

      Public
      Use multiprocessing to generate MD5 checksums using multiple cores
      Python
      •0•0•0•0•Updated Jul 12, 2022Jul 12, 2022

    • minimal_hello_world

      Public template
      Absolute minimum hello world package. Importable and runnable with entry point.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 9, 2021Jul 9, 2021

    • thymesis

      Public
      Message queue that begins with permanent bucket storage
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jun 11, 2021Jun 11, 2021

    • pyweb

      Public
      Docker files for a simple Flask + Gunicorn + nginx stack
      Python
      •
      MIT License
      •0•0•4•0•Updated Apr 14, 2021Apr 14, 2021

    • pycon2020_excel_poster

      Public
      Collaboration for PyCon 2020 poster "Python Powered Excel"
      Jupyter Notebook
      •0•0•0•0•Updated Dec 23, 2020Dec 23, 2020

    • ERCCQC

      Public
      RNASeq ERCC transcript QC metrics
      Java
      •0•0•0•0•Updated Oct 24, 2019Oct 24, 2019

    • prs

      Public
      Polygenic Risk Score calculator and reference data.
      Python
      •0•0•0•0•Updated Aug 25, 2019Aug 25, 2019

    • ngsi-pm

      Public
      Highly customized scrips for working with NGSI metadata.
      Python
      •2•0•4•0•Updated Aug 15, 2019Aug 15, 2019

    • HARLEE_analysis

      Public
      Data and analyses in conjunction with manuscript – Hansen, et al. A Genocentric Approach to Discovery of Mendelian Disease Genes. (2019)
      Jupyter Notebook
      •0•2•0•0•Updated Aug 7, 2019Aug 7, 2019

    • conda_demo_bash

      Public
      Demo of packaging bash scripts with conda
      Shell
      •
      MIT License
      •0•1•0•0•Updated Jun 5, 2019Jun 5, 2019

    • conda_demo_py

      Public
      Demo of a tool written in Python and packaged by conda
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 4, 2019Jun 4, 2019

    • ARBoR

      Public
      ARBoR (Authenticated Resources in a Hashed Block Registry) is an application for tracking the authenticity and lineage of versioned clinical reports even when they are distributed as PDF or paper copies. ARBoR tracks clinical reports as cryptographically signed hash blocks in an electronic ledger file, which is then exactly replicated to many cl…
      HTML
      •
      MIT License
      •1•0•0•0•Updated Apr 26, 2019Apr 26, 2019

    • supervisor-demo

      Public
      Simple example of a config file and job script to demonstrate the use of supervisor
      Python
      •
      MIT License
      •1•0•0•0•Updated Mar 9, 2019Mar 9, 2019

    • qcweb

      Public
      Simple QC plots
      Python
      •
      MIT License
      •0•1•12•0•Updated Feb 6, 2019Feb 6, 2019