Programming for genomics (2015/2016)

Course code
4S003671
Name of lecturer
Giovanni Malerba
Coordinator
Giovanni Malerba
Number of ECTS credits allocated
6
Academic sector
MED/03 - MEDICAL GENETICS
Language of instruction
English
Period
I semestre dal Oct 1, 2015 al Jan 29, 2016.

Lesson timetable

I semestre
Day Time Type Place Note
Thursday 8:30 AM - 10:30 AM lesson Lecture Hall Auletta della Sezione di Biologia e Genetica  
Friday 10:30 AM - 12:30 PM lesson Lecture Hall Auletta della Sezione di Biologia e Genetica  

Learning outcomes

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.

Syllabus

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)

Reference books
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

Assessment methods and criteria

Oral examination

STUDENT MODULE EVALUATION - 2015/2016