Courses and Code

Below is a set of links to teaching materials for a range of applications including microbiome bioinformatics and community ecology statistics, alongside some other materials focussed on programming, data science & ecological statistics.

Bacterial Community Metagenetics

Below is a 2 part course I teach at MSc. level that follows a complete workflow from raw 16S rRNA metagenetic sequencing data all the way through to publication level statistics and DataViz.

The data are from skin swabs of frogs, with a general research goal of understanding associations between skin bacterial community composition and levels of infection with the fungal pathogen Batrachochytrium dendrobatidis

Part 1: Bioinformatics

Code in RMarkdown format and raw fastq files are here

Part 2: Microbial Community Statistics

This section follows directly on from Part 1, but is also self contained in that it comes with all the output from the bioinformatics. SO if you just want to dive straight into the statistics and data visualisation you can start from here. R markdown and post-QC sequencing data are here

Basic Programming in R

TBD