Training course: scRNA-seq Workshop. An introduction to single cell RNA-seq data analysis

Course Description

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: 5 Nov 2025
• Chosen participants will be notified by: 7 Nov 2025
• Course date: 25-28 November 2025

Venue

Sapienza University of Rome google link P.le Aldo Moro, 5 00195 Rome, Italy

Fee

The course does not include any fee. Participants are expected to pay their own travel and accomodation costs (if any).

Selection

A maximum of 15 participants will be selected. Priority will be given to PhD students, followed by early-career researchers and, finally, professionals. Selected participants will be notified by 7 Nov 2025.

Instructors

• Raffaele Calogero, University of Turin, Italy
• Luca Alessandrì, University of Turin, Italy

Scientific/Organising committee

• Raffaele Calogero, University of Turin, Italy
• Loredana Le Pera, ISS, Rome, Italy (ELIXIR-IT Training Platform)
• Allegra Via, Sapienza University, Rome, Italy (ELIXIR-IT Training Platform)

Organising secretary

• 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 Organisers at: elixir.it.iib@gmail.com

Target audience

A maximum of 15 candidates will be selected. The workshop is suitable for life scientists who are new to single cell gene expression technology data analysis. It is open to PhD and Post-Doc research scientists, as well as team leaders and PIs. No prior knowledge of statistics or computing skills is required. However, a basic understanding of R programming is preferred. Prior knowledge of single-cell sequencing technologies is required.

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

Registration

Application Form

Programme