Course content

These materials were part of the ‘Bioinformatics for T-Cell immunology’ course which took place in July 2022. Please refer to the course page and programme to check details about this course and the original programme.

The content table below outlines the different sessions that were included in the course, as well as the format of the materials (slides/videos/practicals) and each session’s trainers. You may proceed through the materials using the arrows at the end of each page, or pick your topic of interest from the table below to skip straight to it.

 Presentation slides –  View or download the slides

 Practicals – View or download the slides, exercises, datasets, analysis scripts and results

Format	Subject	Trainer(s)
	State-of-the-art in T-Cell immunology	Cecilia Domínguez Conde
	Bioinformatics tools and resources for immunology	Anna Lorenc
	R for immunology bioinformatics	Anna Lorenc, Elena Lukyanova, Marta Perez Alcantara
	Single cell RNA-seq analysis
	ScRNAseq bioinformatics	Cecilia Domínguez Conde, Rasa Elmentaite, Elena Lukyanova, Marta Perez Alcantara
	Single Cell Expression Atlas	Nancy George
	Flow cytometry analysis
	Handling cytometry data in R and quality control	Katrien Quintelier and Artuur Couckuyt
	Visualising cytometry data in R	Katrien Quintelier and Artuur Couckuyt
	Computational flow cytometry	Katrien Quintelier and Artuur Couckuyt
	Multiomics data integration
	Multiple ways to integrate multi-omics data – case studies from studying human diseases	Tamás Korcsmáros, Matthew Madgwick and Dezső Módos
	Integration of -omics data	Tamás Korcsmáros, Matthew Madgwick and Dezső Módos
	OmicsDI	Gaurhari Dass
	Multi-omics pathway analyses for immunologic research (Reactome GSA)	Eliot Ragueneau
	Introduction to machine and deep learning analysis
	Machine and deep learning for image data	Craig Russell
	Machine and deep learning for biosynthetic gene clusters (BGCs) discovery	Maaly Nassar
	Genetics of molecular and immune phenotypes	Blagoje Soskic
	High-throughput sequencing: Material sharing, dissemination, and reusability	Maira Ihsan
	Open data and entrepreneurship – a contradiction?	Matthew Hall