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    25 repositories

    • pa-DRS-Crypt4GH-PoC

      Public
      A proof of concept of a DRS Server supporting Crypt4GH
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Sep 16, 2023Sep 16, 2023

    • pa-DRS-Crypt4GH-Client

      Public
      A DRS Client for the PA implementation of the DRS server incorporating Crypt4GH
      Python
      •0•0•0•0•Updated Sep 16, 2023Sep 16, 2023

    • pa-DRS-Crypt4GH-Downloader

      Public
      A tool to download Crypt4GH encrypted data from the PA DRS Server
      Python
      •
      MIT License
      •0•0•1•0•Updated May 24, 2023May 24, 2023

    • pa-TESK

      Public
      GA4GH Task Execution Service Root Project + Deployment scripts on Kubernetes
      Jinja
      •
      Apache License 2.0
      •29•0•0•0•Updated Feb 14, 2023Feb 14, 2023

    • pa-tool-registry-service-schemas

      Public
      APIs for discovering genomics tools, their metadata and their containers
      Shell
      •
      Apache License 2.0
      •18•0•0•0•Updated Jan 24, 2023Jan 24, 2023

    • pa-tesk_api

      Public
      GA4GH TES API Service that translates tasks into Kubernetes Batch API calls
      Java
      •
      Apache License 2.0
      •18•0•0•0•Updated Jan 13, 2023Jan 13, 2023

    • pa-tesk_core

      Public
      Python code that is launched as images into the Kubernetes cluster by tesk-api.
      Python
      •
      Apache License 2.0
      •13•0•0•0•Updated Jan 12, 2023Jan 12, 2023

    • pa-workflow-execution-service-schemas

      Public
      The WES API is a standard way to run and manage portable workflows.
      Apache License 2.0
      •38•0•0•0•Updated Jan 10, 2023Jan 10, 2023

    • pa-cwl-WES

      Public
      Trigger CWL workflows via GA4GH WES and TES
      Python
      •
      Apache License 2.0
      •18•0•0•0•Updated Jan 3, 2023Jan 3, 2023

    • pa-ga4gh-starter-kit-ui

      Public
      Serves user interface for GA4GH starter kit microservices
      JavaScript
      •4•0•0•0•Updated Dec 12, 2022Dec 12, 2022

    • pa-DRS_GA4GH_starter_kit

      Public
      Open, extensible server implementation of the GA4GH Data Repository Service (DRS) specification
      Java
      •
      Apache License 2.0
      •7•0•0•0•Updated Oct 14, 2022Oct 14, 2022

    • pa-data-repository-service-schemas

      Public
      A repository for the schemas used for the Data Repository Service.
      Apache License 2.0
      •53•0•0•0•Updated Oct 10, 2022Oct 10, 2022

    • gatk4-genome-processing-pipeline

      Public
      Workflows used for processing whole genome sequence data + germline variant calling.
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •43•0•0•0•Updated Dec 23, 2020Dec 23, 2020

    • HAWK

      Public
      Hitting associations with k-mers
      C++
      •
      GNU General Public License v3.0
      •20•0•0•0•Updated Nov 22, 2020Nov 22, 2020

    • gatk4-exome-analysis-pipeline

      Public
      This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and Indel discovery in human exome sequencing data.
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •41•0•0•0•Updated Oct 19, 2020Oct 19, 2020

    • gatk4-germline-snps-indels

      Public
      Workflows for germline short variant discovery with GATK4
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •56•0•0•0•Updated Oct 8, 2020Oct 8, 2020

    • SpliceAI

      Public
      A deep learning-based tool to identify splice variants
      Python
      •
      Other
      •161•0•0•0•Updated May 15, 2020May 15, 2020

    • GangSTR

      Public
      A tool for profiling long STRs from short reads
      C++
      •
      GNU General Public License v2.0
      •16•0•0•0•Updated May 7, 2020May 7, 2020

    • five-dollar-genome-analysis-pipeline

      Public archive
      Workflows used for germline short variant discovery in WGS data
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •45•0•0•0•Updated Jul 29, 2019Jul 29, 2019

    • ClinSV

      Public
      Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
      Other
      •8•0•0•0•Updated Jun 26, 2019Jun 26, 2019

    • cnvkit-dnanexus

      Public
      DNAnexus app for CNVkit
      Python
      •
      MIT License
      •4•0•0•0•Updated Apr 12, 2019Apr 12, 2019

    • oidc

      Public archive
      Make XWiki an identity provider that can be reused by any application
      Java
      •
      GNU Lesser General Public License v2.1
      •22•0•0•0•Updated Sep 27, 2018Sep 27, 2018

    • xnat-openid-auth-plugin

      Public archive
      Java
      •
      GNU General Public License v3.0
      •16•1•0•0•Updated May 17, 2018May 17, 2018

    • sso-devise-omniauth-provider

      Public archive
      A devise Omniauth server which handles Single Sign On
      Ruby
      •
      MIT License
      •74•0•0•0•Updated May 16, 2018May 16, 2018

    • eigensoft

      Public
      Experimental EIGENSOFT performance improvements.
      C
      •15•0•0•0•Updated Nov 1, 2014Nov 1, 2014