BioBam organizes Single-Cell Course

BioBam organizes Single-Cell Course

From September 27th to 29th, 2023, BioBam organized a Single-Cell Data Analysis Course as part of the Intercept-MDS Network Training Activities. The course was designed to offer a specialized educational program aimed at providing Ph.D. candidates within the network with essential skills for exploring the intriguing field of single-cell data analysis.

Course Overview

The three-day program immersed participants in the essential aspects of single-cell data analysis, providing a solid foundation in the discipline. Topics covered included raw data preprocessing, quantification, clustering, cell type identification, and conducting differential gene expression and trajectory data analysis.

The course was taught by our colleagues Ángeles Arzalluz-Luque, Marta Benegas Coll, and Priyansh Srivastava, who have been actively involved daily with these types of analyses for several years now.
With their deep understanding of single-cell RNAseq techniques, they offered a comprehensive overview of all data analysis steps, including the particularity of the underlying single-cell protocols and biology.

Ángeles offered insights into R packages for single-cell analysis and guided students through cell type annotation and differential abundance analysis. Marta delved into the nuances of data preprocessing, clustering, and differential expression analysis, and Priyansh, specializing in statistical models for scRNA-Seq data, elucidated trajectory analysis concepts and tools, equipping participants with the skills to infer pseudotime and analyze cellular trajectories using tools like Monocle3.

Course materials can be found here: Intercept-MDS Single Cell Data Analysis Course – Valencia 2023

The final day featured real-world applications, including presentations by Pau Badia and Joanna Ficek-Pascual. Pau, from the University of Heidelberg, explored cell-cell communication analysis, while Joanna from ETH Zurich discussed computational methods for dissecting cancer heterogeneity. Additionally, participants gained insight into practical implementations through demonstrations and discussions on tools like scMasigPro.


The three-day course provided participants with the opportunity to enhance their skills in single-cell data analysis. Through engaging discussions and knowledge exchange, attendees were able to gain theoretical understanding as well as practical experience. It is expected that the Intercept-MDS Single Cell Data Analysis course will equip participants to pursue their academic and research goals effectively.

The Intercept-MDS Single Cell Data Analysis Course demonstrates BioBam’s commitment to advancing bioinformatics and supporting the growth of aspiring researchers by offering specialized education and practical experience, contributing to developing skillsets crucial for shaping the future of biotechnology.


About the Author Paula Cubilles Paula is a versatile professional with a background in visual arts, design, and branding. With her expertise in communication and marketing, Paula brings a creative and strategic approach to BioBam's brand.

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