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    17 repositories

    • 2024-25-working-group

      Public
      Code from the 2024-2025 omics working group examples
      HTML
      •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

    • mibios

      Public
      Python
      •
      MIT License
      •1•0•20•0•Updated Dec 17, 2024Dec 17, 2024

    • GLAMR-ops

      Public
      Things to deploy GLAMR
      Python
      •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • GLAMR_omics_pipelines

      Public
      Multi-omics pipeline for the GLAMR database
      noaa-omics-software
      Python
      •0•6•6•0•Updated Nov 25, 2024Nov 25, 2024

    • 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, Kenya in 2022 and 2023 through NSF IRES Funding.
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 3, 2024Oct 3, 2024

    • GVHD_mouse_metagenomes

      Public
      Python
      •0•0•0•0•Updated Sep 19, 2024Sep 19, 2024

    • 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 Sep 5, 2024Sep 5, 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_Saxitoxin_ADA

      Public
      Python
      •0•0•1•0•Updated Jul 11, 2024Jul 11, 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 blooms."
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 17, 2023Jul 17, 2023

    • scripts

      Public
      Metagenomic pipeline and other general scripts used in the lab.
      microbiologyngs-analysisgeomicrobiologypythonperlumich
      Perl
      •
      GNU General Public License v3.0
      •22•35•2•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 Microcystis colonies harbor distinct bacterial communities that differ by Microcystis oligotype and with time
      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 generating "lowest common ancestor" in meta-omics/next-generation sequencing.
      Perl
      •
      GNU Lesser General Public License v3.0
      •2•0•0•0•Updated Jan 29, 2022Jan 29, 2022