Repositories list

• mibios

  Public
  Python

  •

  MIT License

  •1•0•19•0•Updated Nov 27, 2024Nov 27, 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

• 2024-25-working-group

  Public
  Code from the 2024-2025 omics working group examples

  HTML

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• GLAMR-ops

  Public
  Things to deploy GLAMR

  Python

  •0•0•0•0•Updated Oct 14, 2024Oct 14, 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-analysisgeomicrobiology+ 3pythonperlumich

  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