Geo-omics's repositories
GLAMR_omics_pipelines
Multi-omics pipeline for the GLAMR database
snakemake_profiles
Snakemake profiles for the lab servers and Great Lakes HPC
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
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."
Seike_et_al_2022_Immunity
Code accompanying: *Ambient oxygen levels regulate intestinal dysbiosis and GVHD severity after allogeneic stem cell transplantation* (Immunity, 2022)
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.
WLE-Acidobacteria-Genomes
This repository holds all code and scripts used during the analysis of Acidobacteria MAGs assembled from western Lake Erie Microcystis Blooms
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.