The course is intended for researchers who have basic familiarity with the experimental technologies and their applications in biology, and who are interested in making the step from a user of bioinformatics software towards adapting or developing their own analysis workflows. The four practical sessions of the course will require you to follow and modify scripts in the computer language R.
The course covers a wide range of topics, including but not limited to:
- Introduction to R and Bioconductor
- Elements of statistics: visualization, regression, PCA and other low-dimensional embeddings, statistical tests incl. multiple, classification / supervised machine learning
- RNA-Seq data analysis – bulk and single cell
- Computing with sequences and genomic intervals
- Working with annotation – genes, genomic features, variants, transcripts and proteins
- Gene set enrichment analysis
- MS-based proteomics and metabolomics
- Basics of microbiome analysis
- Experimental design, batch effects and confounding
- Reproducible research and workflow authoring with R markdown
- Package development, version control and developer tools
The course consists of:
- Morning lectures: 20 x 45 minutes: Monday to Friday 8:30-12:00h
- Practical computer tutorials in the afternoons: Mon, Tue, Thu, Fri 13:30-16:30h
- Evening sessions: Mon, Tue 20:30-22:00h
- A hike in the mountains: Wed 14:00-22:00h
All lecture slides and workshop material will be made available during the course and will remain available after the event.
You will work on the labs at your own pace in small groups with expert guidance (all lecturers from the morning sessions plus teaching assistants).
Participants are required to bring their own laptop with the most recent release versions of R and Bioconductor installed: R-4.2.x and Bioconductor 3.15 installed (details will be provided). Please make sure that your computer’s hardware is sufficiently powered (>=8 GB RAM, >20 GB free disk space) and that you have administrator rights. Please set up your computer beforehand; internet connections at the course venue can be slow and unreliable.
One of the afternoons is for a joint cultural and outdoors activity. We plan a trip into the mountains with a (light) walk in the high-alpine area, weather permitting, and delicious local dinner.
|14.00h||We meet at “Casa della Gioventù” and walk 1 min to the bus waiting for us in Via Dante. Please take the underpass to cross “Via Peter Mayr.”|
|14:15h||The bus leaves towards the cable car for Mount Plose.|
|14:45h||The cable car takes us to the top of Mount Plose in about 20-30 min.|
|45-60 min Hiking to RossAlm at 2200 m altitude.|
|18:00h||Social dinner at RossAlm.|
|20:00h||Time to leave! We walk back to the bus from RossAlm.|
|21:00h||The bus takes us back to Brixen.|
- Solid footwear (ideal: hiking shoes or boots)
- Jacket or warm sweater for the descent (it may get quite fresh)
Please note: If you won’t attend the social programme, please let us know at the latest on Monday 20 June via email to info[at]bioconductor.eu