/EBI-workshop---Extracting-information-from-omics-data

Part of the Data-driven approaches to understanding dementia EBI course. The session titled "Extracting information from omics data"

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EBI workshop: Extracting information from omics data

Part of the Data-driven approaches to understanding dementia course. The session titled "Extracting information from omics data"

Lecture

The lecture slides can be found here.

Practical workshop:

Some slides for the practical session here.

We are focusing on the data from: Yu, Min, et al. "Integrative multi-omic profiling of adult mouse brain endothelial cells and potential implications in Alzheimer’s disease." Cell reports 42.11 (2023).

In this workshop we will explore some of this data together.

0. Fork this repo!

/Quick-start guide to how Git works/

Fork the dev branch of this repo to your Github account. This gives you your own copy to play with that doesn't have any impact on this main repository. As we proceed with the analysis we encourage you to make your own notes and comments in the document and commit them as you go.

The Happy Git with R is a great resource for setting up and using Git with R if needed.

Open .Rproj file, this will open RStudio. Open the first script, 01-differential_expression.qmd. Try to load the packages. Use renv::restore() to make sure all the packages are installed.

Make sure you have all the packages that are needed in an renv

1. Let's look at pre-processing of the RNA-Seq and ATAC-Seq from this paper

Slides to follow along.

Next we will get started with some downstream analysis.

2. Try to run the first code block..

Open 01-differential_expression.qmd to start with and try to run the first code block. Ah.. is there any problem? Correct the error and make your first commit!

3. Let's proceed with some analysis to identify the brain-specific endothelial genes

4. Now we have a gene list let's see if any of these genes are enriched in disease GWAS

Go through 02-magma.qmd for this one. Notice the cheeky sneak-peak for the PPI modules?

5. Let's see if groups of genes might work together in regulatory units

Time for protein-protein interaction networks! You'll be surprised to learn it's 03-protein_protein_interactions.qmd for this one :P

6. Is our narrowed down list more biologically meaningful?

7. Make a pull request to this repo!

This whole time you have been commiting notes and comments to your forked version of our code. Now try making a pull request to this repository, we will review the request and either approve or deny it.

The render course website can be found at https://ukdri.github.io/EBI-workshop---Extracting-information-from-omics-data/.