Official Code repository for the "Autumn School for Single Cell-ers" Workshop at GIMM
Each day will be carried by one trainer and you will be able to find the material associated with each Day in the corresponding directory.
Instructor: Miguel Santos, Gulbenkian Institute for Molecular Medicine
You’ll be introduced to single-cell RNA sequencing (scRNA-seq) technology, covering the key principles and workflows involved in processing raw sequencing data into count matrices, and downstream analysis for the identification of cell types. We’ll also guide you through setting up your working environment for the week. In case we have time, there is also a small tutorial on batch integration.
At the end of the day, we will have a dedicated session for group formation and dataset preparation. During this time, you will choose a dataset to work on throughout the week.
Folder with the datasets: https://drive.google.com/drive/folders/1eKHzXlzMcl2pXIkJnLhivk-zyIrE1Kwn?usp=sharing
Instructor: Helena Crowell, Centro Nacional de Análisis Genómico
In the morning, you’ll explore MUSCAT, a powerful tool for multi-sample differential expression analysis. In the afternoon, you’ll be introduced to MiloDE, a framework for differential expression testing that complements MUSCAT.
Instructor: Francisca Gaspar Vieira, Heidelberg University & EMBL-EBI
This session will focus on MOFA, a statistical framework designed for the integration of multiple data modalities and groups of samples. You’ll learn how to apply MOFA to uncover shared and unique biological signals across datasets.
The data for the practical tutorial is available in the following link: https://heibox.uni-heidelberg.de/d/ceaf2baade004a1f8af3/
Instructor: Tomás Gomes, Gulbenkian Institute for Molecular Medicine
You’ll dive into computational approaches for studying cell–cell communication in single-cell data, exploring key tools and strategies to identify and interpret intercellular signaling patterns.
The final day is dedicated to independent analysis and team presentations. Participants will showcase their results, analytical strategies, and insights gained throughout the workshop.
Organizers: Luis GRAÇA, Marc VELDHOEN, Tomas GOMES, Miguel SANTOS, Jean-Christophe LONE, Diogo FONSECA
Support: Sociedade Portuguesa de Immunologia (SPI), Centro Académico de Medicina de Lisboa-CAML, Faculdade de Medicina da Universidade de Lisboa (FMUL), Gulbenkian Institute for Molecular Medicine (GIMM)
Illustrations: Helena Pinheiro https://www.hpinheiro.com/