Bioinformatics in R 2023

by Ivan G. Costa, Tiago Maié, Johannes Schöneich, Martin Grasshoff & Vanessa Kramer

Dates: 30/10- 27/11
Time: 9:30-17:00
Location: MTZ (Pauwelstr 19), Seminar Room at 3rd Floor and Corridor B

In this course, you will learn:

  • basics of R programing language
  • basics of the bioinformatics package Bioconductor
  • steps necessary for analysis of gene expression  microarray and RNA-seq data
  • visualization and statistics in R
  • typical file formats and overview of computational steps for next generation sequencing data

The target audience are biomedical students, who have little or no experience in programming. The course will have a mix of theoretical and hands-on sections, which will include analysis of public expression data deposited in the public domain as Gene Expression Omnibus and The Cancer Genome Atlas.

Schedule

  • 30/10 – Introduction to Programming in R, R Studio and exercises [ slides | handout ]
  • 6/11 – Introduction to Programming in R 2 [ slides | handout ]
  • 13/11 – Basic Analysis of Gene Expression Data / Exercise with public data deposited in Gene Expression Omnibus [ slides | handout ]
  • 20/11 – Advanced Analysis of Gene Expression: / Exercise with analysis of data from The Cancer Genome Atlas [ slides | handout ]
  • 27/11 – Advanced Analysis of Gene Expression: / Exercise with analysis of data from The Cancer Genome Atlas [ slides | handout ]

Computers and Software

Participants should have their own computer have R software pre-installed. Computers should have a minimum of 4GB memory, 3GB of disk space for software installation and 2GB of free space for exercises. Follow these installation instructions. Also, you should download exercise data from here (to come).

Chat channel (discord)

We will use discord as a discussion forum during the course. Through it, we can supervise your work and create a space to ask and answer questions. This will be used during the course so that students can communicate with teaching assistants.

To ensure we can take advantage of the many functions Discord provides (e.g. screen sharing), we’d like to ask you to install and use the client (https://discord.com/) instead of the online version of the app

Please use this link to join the chat-room. 

Registration

The course will be limited to 30 participants.

15 places are reserved for students registered in Medical and Biology degrees of the RWTH (M.Sc. levels). This registration should occur via RWTH Online on a first-come basis.

The remaining places are offered for Ph.D. candidates from the Biomedical Graduate School from Aachen. Participants will be selected based on a motivation letter (maximum of 300 words), where you should describe:

(1) your research,

(2) supervisor and start date of Ph.D. and

(3) why this course is important to your Ph.D.

Please send your application to courses@costalab.org.  Note that further selection criteria (as the limit of Ph.D. candidates per supervisor) will be used if required. Also, candidates with previous attendance to the course or with advanced programming and bioinformatics skills will not be considered.

The deadline for application/registration (all students) is the 1/09/2023.

Literature

  • R. Gentleman, V. Carey, W. Huber, R. Irizarry, S. Dudoit (Eds.) Bioinformatics and Computational Biology Solutions Using R and Bioconductor, Springer, 2005.
  • Pevzner, P., Shamir R., Bioinformatics for Biologist. Cambridge University Press 2011.

Here are some links for those interested in further improving their knowledge in R.