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    83 repositories

    • GBSC_Billing

      Public
      This repository holds the scripts that allow the GBSC to bill its PIs for storage and compute usage on our cluster, cloud services, and bioinformatics consulting.
      Python
      •1•0•14•0•Updated Dec 11, 2024Dec 11, 2024

    • Swarm

      Public
      Swarm: A Federated Cloud Framework for Large-scale Variant Analysis: https://doi.org/10.1371/journal.pcbi.1008977
      Java
      •
      Apache License 2.0
      •0•4•0•0•Updated Jul 19, 2024Jul 19, 2024

    • Hummingbird

      Public
      Hummingbird: Efficient Performance Prediction for Executing Genomic Applications in the Cloud: https://doi.org/10.1093/bioinformatics/btab161
      Python
      •
      Apache License 2.0
      •4•20•4•0•Updated Jul 19, 2024Jul 19, 2024

    • gcp_utils

      Public
      Scripts to manage access to the Google Cloud Platform
      Shell
      •1•1•0•0•Updated May 23, 2024May 23, 2024

    • encode_utils

      Public
      Tools that are useful to any ENCODE submitting group.
      Python
      •
      MIT License
      •12•3•1•0•Updated Jul 6, 2023Jul 6, 2023

    • htan

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Jun 16, 2023Jun 16, 2023

    • trellis-docs

      Public
      Read the Docs source for Trellis data management framework
      Python
      •
      MIT License
      •0•1•1•0•Updated May 5, 2023May 5, 2023

    • hubmap

      Public
      0•0•0•0•Updated Apr 26, 2023Apr 26, 2023

    • pulsar_lims

      Public
      A LIMS for ENCODE submitting labs.
      Ruby
      •1•3•191•10•Updated Apr 21, 2023Apr 21, 2023

    • personal-health-dashboard

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •4•19•0•0•Updated Mar 8, 2023Mar 8, 2023

    • practices

      Public
      MIT License
      •0•0•0•0•Updated Dec 14, 2022Dec 14, 2022

    • sprout

      Public
      Manage multiple Terraform deployment operations
      Python
      •0•0•0•0•Updated Apr 26, 2022Apr 26, 2022

    • AnnotationHive

      Public
      AnnotationHive: A Cloud-based Annotation Engine
      Java
      •5•6•10•0•Updated Apr 10, 2022Apr 10, 2022

    • StanfordDeepMedicine

      Public
      WDL
      •9•1•0•0•Updated Mar 31, 2022Mar 31, 2022

    • env-modules

      Public
      Environment modules
      Roff
      •0•2•0•0•Updated Jan 30, 2022Jan 30, 2022

    • wearable-infection

      Public
      Real-time detection of infection diseases using wearables
      Python
      •
      Apache License 2.0
      •7•13•1•0•Updated Sep 20, 2021Sep 20, 2021

    • stanford-benchmarking-workflows

      Public
      Python
      •
      MIT License
      •1•6•0•0•Updated Mar 10, 2021Mar 10, 2021

    • trellis-mvp-api

      Public
      Specifications for creating APIs to interact with the Trellis Neo4j metadata store
      MIT License
      •0•1•0•0•Updated Jan 28, 2021Jan 28, 2021

    • covid19-wearables

      Public
      0•0•0•0•Updated Jul 17, 2020Jul 17, 2020

    • dockerfiles

      Public
      Dockerfiles for building Docker images.
      Roff
      •0•0•0•0•Updated Jun 23, 2020Jun 23, 2020

    • gbsc_utils

      Public
      DNXNexus Integration Code
      Python
      •0•0•4•0•Updated Jun 5, 2020Jun 5, 2020

    • PHD-Website

      Public
      0•0•0•0•Updated Mar 27, 2020Mar 27, 2020

    • pulsarpy-to-encodedcc

      Public
      Client for submitting experiments in Pulsar LIMS to the ENCODE Portal https://pulsarpy-to-encodedcc.readthedocs.io/en/latest/dcc_submit.html
      Python
      •
      MIT License
      •1•0•0•2•Updated Mar 4, 2020Mar 4, 2020

    • loom

      Public archive
      A tool for running bioinformatics workflows locally or in the cloud.
      Python
      •
      GNU Affero General Public License v3.0
      •8•29•61•0•Updated Dec 13, 2019Dec 13, 2019

    • pulsarpy

      Public
      The official Python client for Pulsar LIMS
      Python
      •
      MIT License
      •1•0•0•0•Updated Aug 6, 2019Aug 6, 2019

    • scgpm_seqresults_dnanexus

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 31, 2019Jul 31, 2019

    • pulsarpy_dx

      Public
      A client for Pulsar LIMS that integrates sequencing results from DNAnexus: https://pulsarpy-dx.readthedocs.io/en/latest/
      Python
      •
      MIT License
      •0•0•0•0•Updated May 15, 2019May 15, 2019

    • sliders

      Public
      Python package for restructuring and formatting text data
      Python
      •2•0•0•0•Updated Mar 11, 2019Mar 11, 2019

    • file_watcher

      Public
      Recursively watches a specified directory for new files.
      JavaScript
      •0•0•0•0•Updated Mar 10, 2019Mar 10, 2019

    • googledrive_bkup

      Public
      Does a customized, recursive backup of the specified directory to Google Drive.
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 27, 2019Feb 27, 2019