Pinned Repositories
2024-25-working-group
Code from the 2024-2025 omics working group examples
GLAMR-ops
Things to deploy GLAMR
GLAMR_omics_pipelines
Multi-omics pipeline for the GLAMR database
Heterotrophic-Bacteria-Dominate-Catalase-Expression-During-Microcystis-Blooms
This repository holds all analysis code and input files for the manuscript in prep: "Heterotrophic bacteria dominate catalase expression during Microcystis blooms."
omics_working_group
scripts
Metagenomic pipeline and other general scripts used in the lab.
snakemake_profiles
Snakemake profiles for the lab servers and Great Lakes HPC
UMRAD
Universal Multi-omics Reference and Alignment Database
UMRAD-taxonomy
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.
WinamGulf_MetaG_2022-2023
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.
Geo-omics's Repositories
Geo-omics/scripts
Metagenomic pipeline and other general scripts used in the lab.
Geo-omics/GLAMR_omics_pipelines
Multi-omics pipeline for the GLAMR database
Geo-omics/omics_working_group
Geo-omics/snakemake_profiles
Snakemake profiles for the lab servers and Great Lakes HPC
Geo-omics/2024-25-working-group
Code from the 2024-2025 omics working group examples
Geo-omics/Characterizing-individual-Microcystis-colony-phycosphere-communities
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
Geo-omics/GLAMR-ops
Things to deploy GLAMR
Geo-omics/H2O2-Incubation-Experiments
R code and input tables that were used to analyze data from H2O2 incubation experiments with western Lake Erie water
Geo-omics/Heterotrophic-Bacteria-Dominate-Catalase-Expression-During-Microcystis-Blooms
This repository holds all analysis code and input files for the manuscript in prep: "Heterotrophic bacteria dominate catalase expression during Microcystis blooms."
Geo-omics/mibios
Geo-omics/Seike_et_al_2022_Immunity
Code accompanying: *Ambient oxygen levels regulate intestinal dysbiosis and GVHD severity after allogeneic stem cell transplantation* (Immunity, 2022)
Geo-omics/UMRAD
Universal Multi-omics Reference and Alignment Database
Geo-omics/UMRAD-taxonomy
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.
Geo-omics/WinamGulf_MetaG_2022-2023
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.
Geo-omics/WLE-Acidobacteria-Genomes
This repository holds all code and scripts used during the analysis of Acidobacteria MAGs assembled from western Lake Erie Microcystis Blooms
Geo-omics/WLE_Saxitoxin_ADA
Geo-omics/GVHD_mouse_metagenomes