IRTG Course - Introduction to R for genomics

Welcome to the IRTG Course - Introduction to R This workshop is meant for individuals with little previous knowledge R.

The course will run over 2 days (Wednesday, 8.12 and Thursday, 9.12) from 10 am - 12.30 pm and 1.30 pm - 5.30 pm.

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Tutors

• Carl Herrmann, Health Data Science Unit Medical Faculty Heidelberg and BioQuant (carl.herrmann@bioquant.uni-heidelberg.de)
• Carlos Ramirez, Health Data Science Unit Medical Faculty Heidelberg and BioQuant (carlos.ramirez@bioquant.uni-heidelberg.de)

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Is this course for me?

In this two-day course, we want to give you an introduction to working with R in simple data analysis tasks; you will learn the basic principles of reading in a data table, doing some descriptive statistics, making nice plots. On the second day, we will focus on a simple single-cell analysis workflow, which will guide you through the first steps of this kind of analysis!

IMPORTANT NOTE!

While we will start at a very basic level, we would strongly encourage absolute beginners, who have never ever worked with R, to complete a very simple online R intro course on DataCamp ("Introduction to R"), which will give you the very basic first concepts on what R is, and how to do some very simple operations with it. We will send you a link so that you can freely register to DataCamp and follow this course.

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Technical pre-requisites

Every participant will work on her/his own laptop. The easiest way to work with R is using the RStudio interface. Please install RStudio Desktop prior to the start of the course:

1. First install R for your operating system; you will find the correct version on this website
2. Once R is installed, you can install the RStudio Desktop version, which you find here
3. You need to install a couple of R packages; you can download the following script. Load it into RStudio, and then hit the Run button at the top to execute it. It should run smoothly!

Please check that you can open RStudio without error message!

Resources

Here is a list of usefull resources if you want to perform basic analysis with R

• Base R cheatsheet
• Basic plots in R
• Seurat tutorials

Slides

Here are the links to the slides

• Day 1 : introduction

• Day 1 : R markdown

• Day 1 : Data types

• Day 1 : Cleanup

• Day 1 : Plots

• Day 1 : Statistical tests

• Day 2 : Introduction to single-cell analysis

Practical parts

Please document your progress in this Google Sheet

Day 1: General introduction - (almost) first steps in R!

On the first day, we will guide you through the first steps of working with R, from reading data to exploratory analysis and basic statistics.

• Part 0 : Objectives
• Part 1 : Rstudio
• Part 2 : Dataframes
• Part 3 : Data cleanup
• Part 4 : Plotting
• Part 5 : Hypothesis tests

Day 2: a simple single-cell RNA-seq analysis workflow

On the second day, we will go through a step by step simple analysis of a small scRNA-seq dataset using the Seurat toolkit. Don't expect to be able to carry a full scRNA-seq analysis after this! This is meant to give you an idea of a typical workflow rather.

• Part 0 : Initial steps
• Part 1 : Introduction to Seurat
• Part 2 : Quality control
• Part 3 : Feature selection
• Part 4 : Dimensional reduction
• Part 5 : Cluster_visualization - UMAP
• Part 6 : Differential expression
• Part 7 : Profiling cells

You can check your results using this form

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Organisation

The course will be online only!

• Lectures will be over Zoom (we will send the link via email prior to the course)
• We will use Discord channels for the practical sessions (register using this link)