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Welcome

Welcome to the CoDaSeq workshop

This was presented at at Exploring Human Host-Microbiome Interactions in Health and Disease, Wednesday September 7th 2016 from 9:30am to 12pm.

Instructors:

Greg Gloor
Professor at the University of Western Ontario
http://ggloor.github.io

And

Ionas Erb
Postdoctoral Fellow at the Centre for Genomic Regulation

Based on a workshop developed by Jean Macklaim (see release V1) https://github.com/jmmack

The Workshop

The intention of this workshop is to give participants a background in Compositional Data Analysis (CoDa) for transcription studies. At the end of the workshop you will have been introduced to CoDa, why you'd use CoDa, and gain hands-on experience using CoDa analysis in R.

The workshop will focus on hands-on application of three main methods.

1. Exploratory data analysis using the compositional PCA biplot which shows the variance in both the samples and the genes on one plot.
2. Determination and removal of outlier samples
3. Examination of differential abundance under a compositional approach using the ALDEx2 tool.
4. Association analysis using the propr tool, including differential association.
5. Visual and exploratory examination of the data

Before the Workshop

Before the course, please read the materials listed on the sidebar for background.

You should already have a working version of R installed on your laptop, and be able to load the required packages (see "Before we start" and "Setup" for instructions)