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.

wle-acidobacteria-genomes

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