The course aims to provide the core skills to manage “big data” in the genomics era.
The course will focus on R programming, basic scripting and data processing.
Specifically we aim to furnish the knowledge to:
- work into a Linux environment and bash scripting
- use R and its libraries for bioinformatic analyses (Bioconductor project)
- collect and collate genetic data from diverse sources
- arranging directories, renaming and archiving files
- convert files from one format into another
- prepare pipelines of commands for repetitive tasks (for instance, same analyses over more samples)
- learn the fundamentals of Perl and Python programming (hacking pre-existing programs to accomplish novel tasks)
The topics will be illustrated using real-life bioinformatic case studies (for instance, GWAS, exome or transcriptome analyses)
| Author | Title | Publisher | Year | ISBN | Note |
| Arnold Robbins, Nelson H. F. Beebe | Classic Shell Scripting: Hidden Commands that Unlock the Power of Unix | O'Reilly Media | 2005 | 0596005954 |
Oral examination
