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

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    26 repositories

    • 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
      •1•7•1•1•Updated Oct 8, 2024Oct 8, 2024

    • SRA_wastewater_lineages

      Public
      Python
      •1•0•6•0•Updated Aug 7, 2024Aug 7, 2024

    • Library-Rapid-Antigen-Test-Manuscript

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 5, 2024Aug 5, 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 Aug 5, 2024Aug 5, 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 congregate settings
      Nextflow
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Jan 11, 2024Jan 11, 2024

    • big-mhc-discovery

      Public
      High-throughput, reproducible pipelines for discovering and annotating novel MHC alleles in WGS data from many species
      0•0•0•0•Updated Nov 3, 2023Nov 3, 2023

    • 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

    • mhc_genotyper

      Public
      MHC Class I and II genotyper for Non-Human primates with high-accuracy short reads
      Python
      •0•0•0•0•Updated Jun 16, 2023Jun 16, 2023

    • snpRelate

      Public
      A Nextflow pipeline for collating SNP panel results and determining parentage
      Python
      •0•0•0•0•Updated Jun 8, 2023Jun 8, 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

    • dholab-configs

      Public
      Configuration files that, when bundled together with your nextflow workflow of choice, can configure scripts for execution on CHTC, dhogal(2), or an iMac desktop of either available architecture.
      0•0•0•0•Updated Jan 24, 2023Jan 24, 2023

    • nf-iWES

      Public
      NextFlow Pipeline for genotyping immunological genes from macaque whole exome sequence data
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 14, 2022Dec 14, 2022

    • 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), 50% for ZIKV+ +ART (n=3), and 100% for ZIKV+ dams -ART treatment (n=5).
      1•0•0•0•Updated Nov 3, 2022Nov 3, 2022

    • E484T-visualizations

      Public
      Data visualization for manuscript on persistent infection that led to globally unique E484T mutation
      R
      •1•0•0•0•Updated Sep 29, 2022Sep 29, 2022

    • prolonged-infection-suppfig1

      Public
      Pipeline for examining Intrahost Nucleotide Variants for Halfmann et al. 2022
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Sep 7, 2022Sep 7, 2022

    • prolonged-infection-suppfig2

      Public
      Pipeline for visually comparing mutations in a persistent SARS-CoV-2 infection with the virus globally
      R
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Sep 7, 2022Sep 7, 2022

    • SARS-CoV-2-Spike-RBD-Analysis

      Public
      Workflow for analyzing SARS-CoV-2 spike RBD amplicon Illumina data.
      Python
      •0•0•0•0•Updated Jul 13, 2022Jul 13, 2022

    • MHC_MiSeq_Genotyping_Databases

      Public
      0•0•0•0•Updated Sep 10, 2021Sep 10, 2021

    • SNAILS

      Public
      Small Nucleic Acid Instrument for Long Sequences
      Python
      •0•3•2•0•Updated Aug 25, 2021Aug 25, 2021

    • Shortreed-et-al-Supplemental-Code

      Public
      Supplemental Information for Characterization of 100 extended major histocompatibility complex haplotypes in Indonesian cynomolgus macaques
      Python
      •1•0•0•0•Updated Nov 15, 2019Nov 15, 2019