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    18 repositories

    • GLAMR_omics_pipelines

      Public
      Multi-omics pipeline for the GLAMR database
      noaa-omics-software
      Python
      •0•6•11•0•Updated Feb 17, 2026Feb 17, 2026

    • 2024-25-working-group

      Public
      Code from the 2024-2025 omics working group examples
      HTML
      •0•0•0•0•Updated Jan 26, 2026Jan 26, 2026

    • mibios

      Public
      Python
      •
      MIT License
      •1•0•34•0•Updated Dec 17, 2025Dec 17, 2025

    • 2016-2022-Western-Lake-Erie-Time-Series-Metagenomics-and-Metabolomics

      Public
      This repository hosts all code, tables, and database information for the manuscript titled, "Diverse Cyanopeptides Follow Distinct Temporal Succession Patterns …
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 3, 2025Nov 3, 2025

    • GLAMR-ops

      Public
      Things to deploy GLAMR
      Python
      •0•0•0•0•Updated Sep 29, 2025Sep 29, 2025

    • GVHD_mouse_metagenomes

      Public
      Python
      •0•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • WLE_Saxitoxin_ADA

      Public
      Python
      •0•0•0•0•Updated Apr 21, 2025Apr 21, 2025

    • H2O2-Incubation-Experiments

      Public
      R code and input tables that were used to analyze data from H2O2 incubation experiments with western Lake Erie water
      0•0•0•0•Updated Mar 10, 2025Mar 10, 2025

    • scripts

      Public
      Metagenomic pipeline and other general scripts used in the lab.
      pythonperlmicrobiologyumichngs-analysisgeomicrobiology
      Perl
      •
      GNU General Public License v3.0
      •22•36•2•0•Updated Jan 24, 2025Jan 24, 2025

    • WinamGulf_MetaG_2022-2023

      Public
      This repository hosts the code and data tables necessary for the analysis in Hart et al. 2024 of metagenomic data collected from the Winam Gulf, Lake Victoria, …
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 3, 2024Oct 3, 2024

    • omics_working_group

      Public
      HTML
      •0•1•0•0•Updated Aug 14, 2024Aug 14, 2024

    • snakemake_profiles

      Public
      Snakemake profiles for the lab servers and Great Lakes HPC
      Python
      •0•1•0•0•Updated Jul 31, 2024Jul 31, 2024

    • WLE-Acidobacteria-Genomes

      Public
      This repository holds all code and scripts used during the analysis of Acidobacteria MAGs assembled from western Lake Erie Microcystis Blooms
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 17, 2023Jul 17, 2023

    • Heterotrophic-Bacteria-Dominate-Catalase-Expression-During-Microcystis-Blooms

      Public
      This repository holds all analysis code and input files for the manuscript in prep: "Heterotrophic bacteria dominate catalase expression during Microcystis bloo…
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 17, 2023Jul 17, 2023

    • Characterizing-individual-Microcystis-colony-phycosphere-communities

      Public
      This repository holds all metadata tables, scripts, and R code for the bioinformatic and statistical analysis associated with the manuscript: Individual Microcy…
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 23, 2023Jun 23, 2023

    • UMRAD

      Public
      Universal Multi-omics Reference and Alignment Database
      Perl
      •
      MIT License
      •3•0•0•0•Updated Feb 8, 2023Feb 8, 2023

    • Seike_et_al_2022_Immunity

      Public
      Code accompanying: *Ambient oxygen levels regulate intestinal dysbiosis and GVHD severity after allogeneic stem cell transplantation* (Immunity, 2022)
      0•0•0•0•Updated Dec 5, 2022Dec 5, 2022

    • UMRAD-taxonomy

      Public
      Lineages of all organisms and vectors curated to conform with taxonomic conventions creating a clean, untangled phylogentic tree to the strain-level. Use for ge…
      Perl
      •
      GNU Lesser General Public License v3.0
      •2•0•0•0•Updated Jan 29, 2022Jan 29, 2022