Skip to content

@ohsu-comp-bio Oregon Health and Science University Computational Biology

Change the repository type filter

All

    Repositories list

    198 repositories

    • seqrepo-rest-service

      Public
      OpenAPI-based REST interface to biological sequences and sequence metadata
      Python
      •
      Apache License 2.0
      •6•0•0•0•Updated Nov 27, 2024Nov 27, 2024

    • funnel

      Public
      Funnel is a toolkit for distributed task execution via a simple, standard API.
      dockerkubernetesgoogle-cloudslurmgridenginega4ghaws-batchpbs-torque
      Go
      •
      MIT License
      •32•121•106•5•Updated Nov 27, 2024Nov 27, 2024

    • helm-charts

      Public
      Helm Charts for deploying various projects in Kubernetes!
      0•0•0•0•Updated Nov 23, 2024Nov 23, 2024

    • vrs-annotator

      Public
      Annotates VCF Variants with VRS IDs
      Jupyter Notebook
      •3•1•0•0•Updated Nov 22, 2024Nov 22, 2024

    • compbio-galaxy-wrappers

      Public
      OHSU Galaxy wrappers.
      Python
      •11•6•0•1•Updated Nov 12, 2024Nov 12, 2024

    • py-tes

      Public
      Python SDK for the GA4GH Task Execution API
      Python
      •
      MIT License
      •10•5•17•2•Updated Nov 5, 2024Nov 5, 2024

    • fence-multipart

      Public
      AuthN/AuthZ OIDC Service
      Python
      •
      Apache License 2.0
      •48•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • syntheVAEiser

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • .github

      Public
      0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

    • docker-centos-slurm

      Public archive
      Slurm Docker Container on CentOS 7
      Shell
      •
      MIT License
      •4•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • homebrew-formula

      Public
      homebrew tap for OHSU Comp Bio tools
      Ruby
      •
      MIT License
      •1•1•0•2•Updated Sep 19, 2024Sep 19, 2024

    • awesome-tes

      Public
      A curated list of awesome GA4GH TES projects and programs
      workflowbioinformaticsreproducible-researchworkflow-enginega4gh
      Creative Commons Zero v1.0 Universal
      •0•1•1•0•Updated Sep 18, 2024Sep 18, 2024

    • idp-backups

      Public
      Steps for backing up, migrating, and restoring IDP data
      Apache License 2.0
      •0•0•0•0•Updated Aug 29, 2024Aug 29, 2024

    • project-template

      Public template
      Example Repo Template for OHSU Comp Bio projects
      Apache License 2.0
      •0•0•0•0•Updated Aug 12, 2024Aug 12, 2024

    • load-testing

      Public
      Browser load testing using k6s
      JavaScript
      •1•1•2•0•Updated Aug 12, 2024Aug 12, 2024

    • gatk4_xml_prepare

      Public
      Tools to auto-create XML files from GATK4 json descriptions.
      Python
      •
      GNU General Public License v3.0
      •3•0•8•1•Updated Jul 30, 2024Jul 30, 2024

    • glasswing-status

      Public
      Uptime/downtime monitor and status page for CBDS
      uptime-monitorstatus-pageupptime
      Markdown
      •
      MIT License
      •0•0•0•0•Updated Jul 22, 2024Jul 22, 2024

    • regulon-enrichment

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•5•0•0•Updated Jul 16, 2024Jul 16, 2024

    • sower

      Public
      Job dispatcher for Kubernetes
      Go
      •
      Apache License 2.0
      •1•1•0•0•Updated Jun 27, 2024Jun 27, 2024

    • drs_downloader

      Public
      Download tool for AnVIL/TDR data identified by DRS URIs and Google
      Python
      •
      Apache License 2.0
      •3•0•0•0•Updated Jun 5, 2024Jun 5, 2024

    • dos_connect

      Public
      Data Object Registry Connect
      Python
      •1•8•17•1•Updated May 8, 2024May 8, 2024

    • bridge2ai-jupyter

      Public
      Docker Image for JupyterHub with restricted download and tensorflow/pytorch
      Dockerfile
      •1•2•1•0•Updated Apr 19, 2024Apr 19, 2024

    • hatchery

      Public
      Go
      •
      Apache License 2.0
      •4•0•0•0•Updated Mar 20, 2024Mar 20, 2024

    • containers

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •7•0•0•0•Updated Mar 4, 2024Mar 4, 2024

    • data-import-test

      Public
      Collection of scripts and documentation for importing S3 data into the Gen3 system
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Mar 1, 2024Mar 1, 2024

    • openapi-test-runner

      Public
      An application allowing the TES servers to test their conformance to TES Specifications
      HTML
      •
      Apache License 2.0
      •6•0•0•0•Updated Feb 20, 2024Feb 20, 2024

    • nextflow

      Public
      A DSL for data-driven computational pipelines
      Groovy
      •
      Apache License 2.0
      •634•0•0•0•Updated Feb 13, 2024Feb 13, 2024

    • hop-covid-models

      Public
      Jupyter Notebook
      •1•0•0•1•Updated Feb 2, 2024Feb 2, 2024

    • decoupleR

      Public
      R package to infer biological activities from omics data using a collection of methods.
      R
      •
      GNU General Public License v3.0
      •24•0•0•0•Updated Jan 23, 2024Jan 23, 2024

    • decoupleRBench

      Public
      Package to benchmark methods from decoupleR
      R
      •
      MIT License
      •7•0•0•0•Updated Jan 23, 2024Jan 23, 2024