David H. O'Connor Lab at University of Wisconsin—Madison
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dairy-hpai-monitoring
dairy-hpai-monitoring PublicReal-Time Monitoring of HPAI Detections in One or More Dairy Products in the United States
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air-metagenomics
air-metagenomics Public archiveAnalysis Pipeline for Minor and Ramuta et al. 2023: Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregate settings
Nextflow 2
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bespoke-reference-datasets
bespoke-reference-datasets PublicHome-brewed reference datasets used across dholab for host and pathogen genomics
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Shortreed-et-al-Supplemental-Code
Shortreed-et-al-Supplemental-Code PublicSupplemental Information for Characterization of 100 extended major histocompatibility complex haplotypes in Indonesian cynomolgus macaques
Python 1
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Repositories
- dairy-hpai-monitoring Public
Real-Time Monitoring of HPAI Detections in One or More Dairy Products in the United States
- bespoke-reference-datasets Public
Home-brewed reference datasets used across dholab for host and pathogen genomics
- 2025-github-website-demo Public
A guide to making GitHub-hosted dashboards with Labkey, Python, Shiny, and Quarto. Mirrored in dholk experiment 31023.
- Lail-et-al-2024-analysis-pipeline Public archive Forked from nrminor/oneroof
Fork of the "oneroof" pipeline for Lail et al. 2024
- SRA_wastewater_lineages Public Forked from DABAKER165/SRA_wastewater_lineages
Legacy repository for the SRA cryptic lineage finder featured in Suarez et al. 2025
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- nanopore-run-info Public
Information your friendly neighborhood bioinformatician will need to help with your Oxford Nanopore run
- iWES-genotyper Public