PLB2020

Materials of the course Programming Laboratory for Bioinformatics 2020-21

This repository contains:

• slides
• exercises

News

!!! Lecture of May 25 will be held from 9am-12pm (CET) !!!

Course contents

The following contents are available in lectures_materials_and_slides directory:

1. Introduction to the course, introduction to Github and R markdown language
2. Basics of R programming
3. Unix Bash programming
4. Introduction to Bioconductor
5. Introduction to NGS data analysis
6. RNA-seq and Differential Expression analysis
7. Introduction to genetic variant analysis
8. Single Cell analysis
9. Enrichment analysis
10. Network analysis

Exercises

The assignments are available in the exercises directory:

1. Basics of R programming - two sets of exercises (in exercises/R_basics)
2. Unix Bash programming - jupyter notebook containing exercises on bash (in exercises/Bash)
3. Bioconductor - three sets of exercises (in exercises/Bioconductor)
4. NGS data analysis
5. RNA-seq and Differential Expression analysis - R scripts with DESeq2 exercises (in exercises/RNAseq-DE )
6. Introduction to genetic variant analysis - single set of exercises (in exrcises/Variant_analysis)
7. Single cell analysis
8. Enrichment analysis - two sets of exercises (in exercises/Enrichment)
9. Network analysis - one set of exercises (in exercises/Network_analysis)