Little Rock January 2024 Multiomics Demo
Course materials
The code notebooks are already pre-loaded on the Posit Cloud workspace in both .Rmd (source code) and .html (generated output including figures) format. All necessary data is also pre-loaded on Posit Cloud. I have posted all materials here as well, in case people want to access them after the workshop when the Posit Cloud workspace is no longer available.
- Introductory slides
- Demo 1: Multi-omics factor analysis (MOFA) | Rmd | HTML
- Demo 2: MOFA application | Rmd | HTML
- Demo 3: sPLS-DA analysis with mixOmics | Rmd | HTML
- Data needed to run all the demos (.zip)
Video recording of omics workshop will be shared with participants by email.
Pre-workshop instructions
You have two options for following along with the code in the workshop.
Option 1: I have created a project on Posit Cloud. You can run the R code on the cloud server without installing anything on your own computer. All you have to do is sign up for a Posit Cloud account (already paid for by the Area Office), join the project group, and create your own copy of the project template. Participants will receive an invitation link by email. Instructions for signing up for an account and joining the project are here.
The Posit Cloud server is only for demonstration and teaching purposes. It is not secure. NO GOVERNMENT-OWNED DATA MAY BE UPLOADED TO THIS SERVER.
Option 2: Install R, RStudio, all necessary R packages, and set up a Python virtual environment within R on your own computer. We will not have time during the workshop to troubleshoot any installation issues that may arise. However, if you want to analyze your own data with the methods you learn in the workshop, you will eventually need to install this software locally or run it on the SciNet cluster. Instructions on how to install R, RStudio, R packages, and set up a Python virtual environment on your own computer are here. Note you will only need to follow steps 1 and 2 on the linked page and then run the provided omics workshop setup script in RStudio.
Post-workshop survey
Please help me improve future trainings by telling me what you thought about this workshop! Google Forms feedback survey
Page last updated 2024-01-09