Tuesday May 23 – Practicals I: Downstream Bulk Retrotranscriptomics
| Time | Event | Speaker |
|---|---|---|
| 9:00 AM - 9:20 AM | Coffee + Log in to RStudio | Dr. Matthew Bendall |
| 9:30 AM - 10:30 AM | Unsupervised Principal Component Analysis (PCA) | Bhavya |
| 10:30 AM - 11:00 AM | Coffee break | Coffee speaks for itself |
| 11:00 - 12:00 AM | Differential expression analysis using DESeq2 | Bhavya |
| 12:00 - 1:00 PM | Performing Gene-set enrichment analysis | Bhavya |
| 1:00 PM - 2:30 PM | Lunch | Ordered at Belfer |
| 2:30 PM - 3:30 PM | Performing rTWAS | Dr. Rodrigo Duarte |
| 3:30 PM - 4:00 PM | Indian Tea and Biscuits | Parle-G |
| 4:00 PM - 4:30 PM | Performing rTWAS | Dr. Rodrigo Duarte |
| 8:00 PM - TBD | Meet at Sour Mouse (East Village) for drinks and games (optional) | Sour Mouse |
Log into AWS as per Matthew Bendall's tutorial from yesterday, and symlink this entire directory into your home directory. All you really need are the the results, refs, and fgsea directories, but if you symlink the entire directory (as suggested), you'll be able to access intermediate files in case one of the commands fails (I hope not though!)
ln -s /efs/projects/tea-biscuit-retro/ tea-biscuit-user
cp /efs/projects/tea-biscuit-retro/tutorial.R .
Open the tutorial.R file, head on over to our actual tutorial, and you're good to go!
Ask Bhavya for secret link to download (sorry, cannot post the link here).
You can open tutorial.R and copy-paste commands from the tutorial.md or .html file. Or, you can open the tutorial.Rmd and just run things with me.
If you want to create your own R script: File -> New File -> R Script. Follow along by copying and pasting from the tutorial.md file.
You can simply follow along and watch. There is no pressure! Play along however you see fit.