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***This course is fully booked*** This interactive online MSD Skills training course is aimed at DPhil students, postgraduate research students and any other staff who would like to learn how to analyse RNA-Seq data using R.

You will need to attend two sessions, one in the morning 10:00 - 12:00 and second in the afternoon 13:00 - 15:00.


This course is aimed at those with minimal or no previous experience analysing RNA-Seq data and will cover key steps including data quality checks, formatting data and running differential expression analysis in R. The majority of the time will be spent on practical guided tutorials that cover the analysis steps in detail with an example cancer dataset. Familiarity with R programming is beneficial but not essential (all necessary code will be provided).

Please make sure you read all of the sections below relating to how the course will work, and the survey and attendance certificate policy.



By the end of this course, you will learn:

  • key steps and considerations for processing and analysing RNA-Seq data
  • ways to assess data quality and identify potential issues
  • how to prepare a dataset for analysis
  • how to perform differential expression analysis  


The course is structured into 2 separate sessions, each of 2 hours (with breaks and time for questions/discussion):

Session 1 – Introduction to RNA-Seq; Practical 1: Assessing data quality

Session 2 – Practical 2: Data preparation; Practical 3: Differential expression analysis







The sessions will be held online, and you will sent a link and joining instructions beforehand. You will also receive a link in the booking confirmation and reminder emails to use during the sessions through which you can access course materials such as scripts and markdown notebooks. We will give some introduction and time to ensure everyone is set up to start the interactive parts of the course. To help things run smoothly, there will be an assistant instructor who will help answer queries in the chat or resolve any issues an individual participant may encounter.


We will aim to run through the course working on each practical together as a group. Timings for each section will be flexible to cater to the group attending and give time for discussion and questions. There will be a mixture of instructor demonstration and sections where you can follow the guided tutorial at your own pace. Instructors will be available for ~30 mins after each session for anyone wanting additional time or help to complete the practical exercises.



Software and hardware requirements:

A personal laptop or computer with R software installed, internet connection and access to Microsoft Teams. The current version of R is v4.1.0 but any recent version should be fine. The RStudio (Desktop) interface is also recommended for the functionality it offers.

R and RStudio can be downloaded for any operating system from the following links:

If you have not used R before

We strongly recommend looking at our introductory tutorials at the link below:

If you are comfortable using the R environment and pasting pre-written code into R, that is sufficient background for attending this course - you will be able to follow the tutorial steps even if you don’t understand all the details of the code and syntax. However, if you have never used R before, you may find you get more from attending this course at a future date when you have had time to familiarise yourself with the R environment. We are happy for novice R programmers to join this course, although please note that we will not be able to spend much (if any) time addressing queries or issues to do with basic R functionality or commands during the course.



Once you have completed the course, you will be sent an email with a link to the overall course survey. When you have filled in and submitted the survey, you will be sent an email with a link to your attendance certificate. This is to ensure we receive the feedback we need to evaluate, improve our courses and plan the follow-up modules. Survey results are downloaded and stored anonymously.



Where there is no cost in the shopping trolley, no deposit is required. However, more than two consecutive non-attendances or late cancellations without good reason will be logged and may mean you cannot attend any further MSD training that term. Please refer to our Terms and Conditions for further information.