Repositories list

• mibios

  Public
  Python

  •

  MIT License

  •11 fork•00 stars•3434 issues•11 pull request•Updated Sep 4, 2026Sep 4, 2026

• 2024-25-working-group

  Public
  Code from the 2024-2025 omics working group examples

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 17, 2026Aug 17, 2026

• GLAMR-ops

  Public
  Things to deploy GLAMR

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 4, 2026Aug 4, 2026

• GLAMR_omics_pipelines

  Public
  Multi-omics pipeline for the GLAMR database. Documentation: https://geo-omics.github.io/GLAMR.docs

  noaa-omics-software

  noaa-omics-software

  Python

  •00 forks•66 stars•1010 issues•00 pull requests•Updated Jul 30, 2026Jul 30, 2026

• CyanopeptideMatchingPythonVersion

  Public
  Cyano detection algorithm with outputs for data analysis

  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 6, 2026May 6, 2026

• 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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 3, 2025Nov 3, 2025

• GVHD_mouse_metagenomes

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 8, 2025Jul 8, 2025

• WLE_Saxitoxin_ADA

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•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

  00 forks•00 stars•00 issues•00 pull requests•Updated Mar 10, 2025Mar 10, 2025

• scripts

  Public
  Metagenomic pipeline and other general scripts used in the lab.

  pythonperlmicrobiology+ 3

  pythonperlmicrobiologyumichngs-analysisgeomicrobiology

  Perl

  •

  GNU General Public License v3.0

  •2222 forks•3636 stars•22 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 3, 2024Oct 3, 2024

• omics_working_group

  Public
  HTML

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 14, 2024Aug 14, 2024

• snakemake_profiles

  Public
  Snakemake profiles for the lab servers and Great Lakes HPC

  Python

  •00 forks•11 star•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 23, 2023Jun 23, 2023

• UMRAD

  Public
  Universal Multi-omics Reference and Alignment Database

  Perl

  •

  MIT License

  •33 forks•00 stars•00 issues•00 pull requests•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)

  00 forks•00 stars•00 issues•00 pull requests•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

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jan 29, 2022Jan 29, 2022