This page contains the information and materials of the OMICS workshop.
The idea of this workshop is to make the students familiar with the basic tools to perform different OMICS analyses. We will start with a general introduction to Python and R allowing the students to write their own programs for their analyses. Additionally we will provide an overview over existing programs in the area of differential expression and orthology detection.
Part 1: Linux and Python (20-24.11)
Responsible: Elias Dohmen, Carsten Kemena
Day | Lecture | Short Description | Exercise | Data (needed for Exercises) | Materials |
---|---|---|---|---|---|
1 | Linux Introduction | Introduction to basic Linux commands | Exercise
Solutions |
Data | |
2 | Python 1 | Basics of programming in Python (variables, loops, compare basic conditions) | Exercise | ||
3 | Python 2 | Strings and functions are introduced and how they are used to read/write from/to files | Exercise | ||
4 | Python 3 | Further important pre-existing data types like dict, set etc. are introduced | Exercise | Data | |
5 | Python 4 | ErrorHandling and modules from the standard library are introduced | Exercise | Data |
Part 2: Statistics and Visualization in R (27-28.11)
Responsible: Evelien Jongepier
Requirements: Basic stats knowledge
Day | Lecture | Short Description | Exercise | Data (needed for Exercises) | Materials |
---|---|---|---|---|---|
6 | R basics lecture | R syntax and data types | R basics exercises | ||
7 | R plots lecture | R data analyses and visualization | R plots exercises | GEOdata |
Part 3: Transcriptomics (29-30.11)
Responsible: Evelien Jongepier
Requirements: Basic Bash knowledge, Basic R knowledge
Day | Lecture | Short Description | Exercise | Data (needed for Exercises) | Materials |
---|---|---|---|---|---|
8 | Transcr lecture | Transcriptome assembly using Trinity | Transcr exercises | RNAseq data | |
9 | DE lecture | Differential expression analyses using DESeq2 | DE exercises | DE data |
Part 4: Proteomics and Orthology (4-6.12)
Responsible: Elias Dohmen, Evelien Jongepier, Carsten Kemena
Requirements: Basic Linux knowledge, Basic R knowledge for the enrichment analysis
Day | Lecture | Short Description | Exercise | Data (needed for Exercises) | Materials |
---|---|---|---|---|---|
10 | Orthology | Orthology clustering in the context of genomes and proteomes. | Exercise Orthology | ||
11 | Protein Domains | Proteomics with Protein Domains as Markers for Protein Orthology. | Exercise Domains | results_Danio_rerio.pfam | |
12 | Enrichment lecture | GO-term analysis and visualization | Enrichment exercises |
Part 5: Bring your own data (7-8.12)
This section is dedicated to helping you with problems you have with your own data. You can bring your own data and we will help you with questions concerning the topics we covered in this course.