💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
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Updated
Jan 12, 2024 - Python
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Tools for visualising microbial community amplicon data
Various functions for analysis of microbial community data
Super snazzy online phylogenetic tree viewer with automatic customization using simple, tab-separated text files.
creating hybrid-gene phylogenetic trees for diversity analyses
Materials and presentation for the 2022 ISB Microbiome course.
Materials and presentation for the 2023 ISB Microbiome course.
📦BEEM-Static: An R package for inferring microbial interactions based on Lotka-Volterra models
Microbiome data simulator for power analysis
Comparative Metatranscriptomics Workflow
Environmental metagenomics, Spring 2022, Physalia Courses
Environmental metagenomics, Spring 2023, Physalia Courses
lake itag measurements over nineteen years
A metadata schema for the Minimum Information about Intermicrobial Interaction Data (MIIID) using LinkML
A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
Easy-to-use tool facilitating work with Mothur.
My personal research website
A simple package for simulations of microbial growth experiments with realistic sources of error.
Data and code for LaMartina et al., 2021
Supplemental code of the paper "Environmental selection shapes the formation of near-surface groundwater microbiomes".
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