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@dholab David H. O'Connor Lab at University of Wisconsin—Madison

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    Repositories list

    37 repositories

    • nhp-immunogenomics

      Public
      NHP immunogenomics resources maintained by the O'Connor lab as part of a NIAID-funded MHC contract and in support of the Wisconsin National Primate Research Cen…
      Python
      •0•0•0•0•Updated Sep 10, 2026Sep 10, 2026

    • gid-seminars

      Public
      Global infectious disease virtual seminar/webinar finder
      Python
      •0•0•0•0•Updated Sep 10, 2026Sep 10, 2026

    • nvd

      Public
      Opinionated viral metagenomics workflow
      Python
      •
      GNU General Public License v3.0
      •4•17•12•1•Updated Sep 9, 2026Sep 9, 2026

    • team-canada-world-cup-2026

      Public
      Interactive manuscript + submission PDF for the Team Canada air-sampling study (2026 FIFA World Cup).
      HTML
      •0•1•0•0•Updated Sep 4, 2026Sep 4, 2026

    • dairy-hpai-monitoring

      Public
      Real-Time Monitoring of HPAI Detections in One or More Dairy Products in the United States
      Python
      •
      GNU General Public License v3.0
      •2•9•0•0•Updated Sep 4, 2026Sep 4, 2026

    • baits

      Public
      Identify diagnostic sequence baits for your taxa of interest
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 30, 2026Aug 30, 2026

    • cyclospora-in-wastewater-metagenomics

      Public
      Evidence for cyclospora rRNA in metagenomic wastewater datasets
      Python
      •0•1•0•0•Updated Aug 28, 2026Aug 28, 2026

    • common-densoviruses

      Public
      Common densoviruses in the human and mammalian virospheres
      Python
      •1•1•0•0•Updated Aug 25, 2026Aug 25, 2026

    • nao-mgs-workflow-chtc

      Public
      CHTC fork of NAO MGS workflow used by SecureBio
      Python
      •
      MIT License
      •11•0•0•0•Updated Mar 1, 2026Mar 1, 2026

    • SARS-CoV-2-in-pregnancy-public

      Public
      Public content from the SARS-CoV-2 in pregnancy project
      0•1•0•0•Updated Feb 24, 2026Feb 24, 2026

    • geneious-plugin-sra-search

      Public
      NCBI SRA Search plugin for Geneious Prime - Search and download SRA datasets directly in Geneious
      Java
      •
      Other
      •0•1•0•0•Updated Nov 19, 2025Nov 19, 2025

    • htcondor_basecalling

      Public
      Shell scripts, submit files, and dag files for basecalling Oxford Nanopore signal files on CHTC's HTCondor cluster
      Shell
      •
      MIT License
      •0•1•0•0•Updated Sep 30, 2025Sep 30, 2025

    • mhc_genotyper

      Public
      MHC Class I and II genotyper for Non-Human primates with high-accuracy short reads
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Sep 24, 2025Sep 24, 2025

    • 2025-github-website-demo

      Public
      A guide to making GitHub-hosted dashboards with Labkey, Python, Shiny, and Quarto. Mirrored in dholk experiment 31023.
      Just
      •
      MIT License
      •0•0•0•0•Updated Feb 17, 2025Feb 17, 2025

    • allele-discovery

      Public
      A Snakemake workflow for discovering novel alleles with PacBio HiFi reads
      Python
      •
      MIT License
      •1•0•1•0•Updated Feb 13, 2025Feb 13, 2025

    • Lail-et-al-2024-analysis-pipeline

      Public archive
      Fork of the "oneroof" pipeline for Lail et al. 2024
      Python
      •
      MIT License
      •4•0•0•0•Updated Jan 3, 2025Jan 3, 2025

    • SRA_wastewater_lineages

      Public
      Legacy repository for the SRA cryptic lineage finder featured in Suarez et al. 2025
      Python
      •1•0•6•0•Updated Dec 18, 2024Dec 18, 2024

    • air_qpcr_helpeR

      Public
      Shiny apps that help work with virus qPCR data from air sample cartridges
      R
      •
      Other
      •0•0•0•0•Updated Dec 5, 2024Dec 5, 2024

    • Library-Rapid-Antigen-Test-Manuscript

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • nanopore-run-info

      Public
      Information your friendly neighborhood bioinformatician will need to help with your Oxford Nanopore run
      0•0•0•0•Updated Oct 25, 2024Oct 25, 2024

    • iWES-genotyper

      Public
      Python
      •0•0•0•0•Updated Jul 26, 2024Jul 26, 2024

    • IPD-ref-generator

      Public
      Workflow for generating useful immunological gene allele databases
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 11, 2024Jun 11, 2024

    • embl-my-gbk

      Public
      Convert a Genbank file with many extraneous Geneious annotations to EMBL format (even with of strict requirements as IPD)
      Python
      •
      MIT License
      •2•0•0•0•Updated Mar 22, 2024Mar 22, 2024

    • IPD-converter

      Public archive
      Nextflow pipeline for converting annotated, genbank-formatted novel allele sequences to Immuno Polymorphism Database format
      Nextflow
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 10, 2024Mar 10, 2024

    • air-metagenomics

      Public archive
      Analysis Pipeline for Minor and Ramuta et al. 2023: Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregat…
      Nextflow
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Jan 11, 2024Jan 11, 2024

    • AVRL-pango-updator

      Public
      Nextflow Pipeline for Updating and Extending SARS-CoV-2 Lineage Classifications
      Nextflow
      •
      Other
      •0•0•0•0•Updated Jun 19, 2023Jun 19, 2023

    • nf-templates

      Public
      Simple NextFlow Templates for Developing your own Workflows
      Nextflow
      •1•0•0•0•Updated Mar 14, 2023Mar 14, 2023

    • MHC-II-allele-discovery

      Public
      Nextflow pipeline for discovering new MHC Class II alleles in Rhesus and Cynomolgus Macaques
      Nextflow
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Feb 27, 2023Feb 27, 2023

    • Mecklenburg-et-al-2022

      Public
      Data and scripts used to confirm the discovery of a new cynomolgus macaque Hepatitis A virus
      Python
      •0•0•0•0•Updated Feb 15, 2023Feb 15, 2023

    • Frequent-first-trimester-pregnancy-loss-in-rhesus-macaques-infected-with-African-lineage-Zika-virus

      Public
      We found that infection with 1X10^4 PFU ZIKV-DAK at GD30 resulted in pregnancy loss between GD 42 and GD 51 with rates of 100% for SIV+/ZIKV+ dams +ART (n=3), 5…
      1•0•0•0•Updated Nov 3, 2022Nov 3, 2022
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