Bioinformatics for T-Cell immunology - Single Cell Expression Atlas - Part 3 (web link)

Overview:This hands-on session will be split into two parts, and will give you the chance to analyse different single cell RNA sequencing data objects.

Learning outcome
By the end of this session you will be able to:

• Perform quality control and data normalisation
• Perform dimensionality reduction (PCA, UMAP) and clustering
• Perform batch correction using BBKNN
• Use automated cell type annotation (CellTypist)
• Prepare data for the use with different tools (CellphoneDB)
• Read and explore single-cell VDJ data contained in contig annotation files
• Integrate single-cell RNA expression and single-cell VDJ data
• Quality control and interpretation of scTCR-seq data based TCR chain combinations detected
• Determine the usage of V(D)J gene segments across cell types and cell states
• Identify clonotypes using several parameters, determine clonal expansion and repertoire overlap across conditions

Cecilia Domínguez Conde – Human Technopole

Cecilia Domínguez Conde is a Group Leader at the Population & Medical Genomics programme of the Genomics Centre. After training as a pharmacist in the University of Seville, Cecilia went on to do a PhD in Immunology at the Research Centre for Molecular Medicine (CeMM) in Vienna where her work focused on dissecting the genetic cause of molecularly undiagnosed primary immunodeficiencies using exome sequencing. In 2019 Cecilia joined the Teichmann lab at the Wellcome Sanger Institute where her focus has been to dissect the diversity of human immune cell types across lymphoid and non-lymphoid tissues as part of the Human Cell Atlas initiative. Her research group at HT uses cutting-edge genomic technologies to study developmental immunology.

Rasa Elmentaite – Wellcome Sanger Institute

Staff scientist in Sarah Teichmann’s team at Wellcome Sanger Institute.