This course offers a comprehensive introduction to single-cell RNA sequencing (scRNA-seq) data analysis using open-source tools, with a focus on the rCASC package https://github.com/kendomaniac/rCASC. Participants will delve into experimental design principles, quality control for single-cell sequence outputs, and data reduction and clustering techniques to identify cell subpopulations. The course also offers an overview of the computational theory behind scRNA-seq tools, empowering participants to make informed decisions during analysis. Practical, hands-on sessions will allow attendees to work with real datasets and integrate results to extract meaningful biological insights.
Important Dates
- Deadline for applications: 20th January 2025
- Chosen participants will be notified by: 27th January 2025
- Course date: 10-12 February 2025
Fee
The course includes a fee of 150 Euros for academic attendees and 400 Euros for industry professionals. Participants are expected to pay their own travel and accommodation costs (if any).
Selection
A maximum of 20 candidates will be selected on a first-come- first-served basis. Selected participants will be notified by 27th January 2025.
Instructors
- Raffaele Calogero, University of Turin, Italy
- Luca Alessandrì, University of Turin, Italy
Helpers
- Ernesto Picardi, University of Bari, Italy
- Adriano Fonzino, University of Bari, Italy
- Pietro D’Addabbo, University of Bari, Italy
Scientific/Organising committee
- Raffaele Calogero, University of Turin, Italy
- Ernesto Picardi, University of Bari, Italy
- Loredana Le Pera, ISS, Rome, Italy (ELIXIR-IT Training Platform)
- Allegra Via, Sapienza University, Rome, Italy (ELIXIR-IT Training Platform)
- Francesca De Leo, CNR, Bari, Italy
- Graziano Pesole, University of Bari, Italy
Organising secretary
- Marilena D’Ambrosio, CNR, Bari, Italy
- Chiara Bruno, CNR, Italy
- Gianmarco Pascarella – CNR, Italy (ELIXIR-IT Training Platform)
- Irene Artuso, ISS, Rome, Italy (ELIXIR-IT Training Platform)
Contact
For all kinds of queries, please contact the Local Organizers at: elixir.it.iib@gmail.com
Aims of the workshop
- Introduce the principles and importance of designing effective scRNA-seq experiments.
- Guide participants through quality control, data reduction, and clustering methods for scRNA-seq data.
- Provide hands-on experience to develop practical analysis skills and enable the extraction and interpretation of biological insights from scRNA-seq datasets.
Resources and tools covered
rCASC package for scRNA-seq analysis (https://github.com/kendomaniac/rCASC)
Learning Outcomes
By the end of this course, participants will be able to:
- Describe the importance of experimental design to ask sensible biological questions at single cell level.
- Assess the quality of your data.
- Describe limits and strength of clustering in scRNA-seq.
- Identify genes driving cluster formation in scRNA-seq.
- Annotate cell types
- Performe batch correction and experiment integration on scRNA-seq data.
Course prerequisites
Before starting the course, participants are requested to follow a brief and simple course on R, approximately 4 hours. The video lessons and lesson pdfs with exercises are available at https://bit.ly/47XmDwx