geo-omics Goto Github PK

2023_metagenomics_working_group

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

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."

mibios

scripts

Metagenomic pipeline and other general scripts used in the lab.

seike_et_al_2022_immunity

Code accompanying: *Ambient oxygen levels regulate intestinal dysbiosis and GVHD severity after allogeneic stem cell transplantation* (Immunity, 2022)

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.

wle-acidobacteria-genomes

This repository holds all code and scripts used during the analysis of Acidobacteria MAGs assembled from western Lake Erie Microcystis Blooms

wle_saxitoxin_ada