microbial-ecology

💎 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

The Biosynthetic Gene cluster Meta’omics abundance Profiler (BiG-MAP). A command-line tool that is able to profile the abundance and expression of a collection of gene clusters across metagenomic and metatranscriptomic data from any kind of biome, including human, plant, animal, marine, and soil microbiomes.

creating hybrid-gene phylogenetic trees for diversity analyses

Super snazzy online phylogenetic tree viewer with automatic customization using simple, tab-separated text files.

Materials and presentation for the 2022 ISB Microbiome course.

Materials and presentation for the 2023 ISB Microbiome course.

Metabolic modeling tutorial for EMBO practical course: Metabolite and species dynamics in microbial communities 2022

Microbial Culture Media Knowledge Graph - Comprehensive collection of 10,000+ culture media recipes from major international repositories with LinkML schema, ontology grounding, and browser-based exploration

Comparative Metatranscriptomics Workflow

📦BEEM-Static: An R package for inferring microbial interactions based on Lotka-Volterra models

Microbiome data simulator for power analysis

Environmental metagenomics, Spring 2023, Physalia Courses

Environmental metagenomics, Spring 2022, Physalia Courses

lake itag measurements over nineteen years

Visualize deep ocean biogeochemical sediment samples in 2D and 3D

A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.

A metadata schema for the Minimum Information about Intermicrobial Interaction Data (MIIID) using LinkML