Official Code repository for the "The Hitchhiker's Guide to scRNA-seq" Workshop at iMM
Use this Google Drive for any questions and interactions during the WOrkshop
https://drive.google.com/drive/folders/1Eb_yre1mUSxM_xhzcVRs_urtw0gXEc8g?usp=share_link
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. Some files exceeding 25 MB will be availble thru other means.
Trainer: Tomas Gomes, Instituto de Medicina Molecular
This day, you will be introduced to the single cell RNAseq technology (scRNAseq) as well as their general means to analyse the raw data generated by the sequencers to the count matrices. We will also help you te set up your working environment.
Programming languages: Python, R
Trainer: Antonio Sousa, University of Turku
This day, you will learn how to integrate several dataset together to find a common space in which the different cells type can be understood with a common ground.
Programming languages: R
Trainer: Lisa Dratva, Sanger Institute & Stem Cell Institute Cambridge)
You will learn how to analyse a specific type of scRNAseq dataset with the T cell Receptor of some immune cells called T cells. In addition to the gene expression (GEX) some immune cells can be types using this receptor's sequence (VDJ)
Programming languages: Python
Trainer: Zhisong He, ETH Zurich
You will learn how to perform pseudotime and trajectory analysis.
Programming languages: Python and R
Trainer: Anna Maguza, Würzburg Institute of Systems Immunology
Introduction to spatial transcriptomic
Link to the practical part 1 (squidpy) - https://colab.research.google.com/drive/1h5_7uNIVSuJ9UfhkVlauP3Kmwj3b04EY?authuser=2#scrollTo=ThAkw4NrHx0j
Link to the practical part 2 (cell2location) - https://colab.research.google.com/drive/1U-CkXyWiiOA-3xg1w1VrrDE7SY7zTbyP?usp=sharing
Programming languages: Python
Organizers: Diogo FONSECA, Tomas GOMES, Luis GRAÇA, Jean-Christophe LONE, Miguel SANTOS, Marc VELDHOEN, Rui VIEIRA
Support: MSC-ITN ENLIGHT-TEN+, Sociedade Portuguesa de Immunologia (SPI), Centro Académico de Medicina de Lisboa-CAML, Faculdade de Medicina da Universidade de Lisboa (FMUL), EFIS-IL study group T CELL CONNECT EUROPE (TCC_EUROPE)
Funding Agency: This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No.: 955321
Illustrations: Helena Pinheiro https://www.hpinheiro.com/