Bioinformatics in R (BiR)

by Ivan G. Costa, Joseph Kuo, Fabio Ticconi, Zhijian Li & Tiago Maie

This practical block course will provide students basics of R programming and how to use R to perform simple analysis of gene expression and other omics data.

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 programing. 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

  • Day 1 – Introduction to Programming in R, R Studio and exercises [slides]
  • Day 2 – Basic Analysis of Gene Expression Data / Exercise with public data deposited in Gene Expression Omnibus
  • Day 3 – Advanced Analysis of Gene Expression: / Exercise with analysis of data from The Cancer Genome Atlas
  • Day 4 – Visualization and Statistics with R / Exercises
  • Day 5 – NGS data and visualization with IGV

Registration

The course will be limited to 18 participants. Half of the places are reserved for students registered in Medical and Biomedical degrees of the RWTH (B.Sc and M.Sc. levels). These registration should occur via Campus in a first come basis.

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 limit of Ph.D. candidates per supervisor) will be used if required. Also, candidates with advanced programing and bioinformatics skills will not be considered.

The deadline for application/registration (all students) is the 15/9/2018.

Computers and Software

Participants should bring their own laptops and have R software pre-installed.  We will send you installation instructions before the course.

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.

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