Bioinformatics for T-Cell immunology-R for immunology bioinformatics

Overview:This short practical session will facilitate participants’ active participation in the hands-on parts of the course.

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

• Access RStudio and Jupyter Notebooks on the course virtual machines
• Use R to follow and undertake the data analysis provided during this course.
• Use Python to follow the data analysis provided during this course.

Anna Lorenc – Wellcome Sanger Institute

Anna is a computational biologist in Gosia Trynka’s lab of Immune Genomics at Wellcome Sanger Institute, which she joined after 7 years at Kings College London in the Adrian Hayday and Mark Peakman labs. Her scientific interests are T cell receptors in the context of autoimmune diabetes. She has experience in analysing diverse immunological datasets, from high throughput flow cytometry to scRNAseq and bulk TCR sequencing. She is a big fan of R, Bioconductor, open science and wet lab scientists developing computational skills.

Marta Perez Alcantara – Wellcome Sanger Institute

Post doctoral fellow in the immune genomics group. I study the genetics of neurodegenerative disease (particularly Alzheimer’s disease) and how it affects microglial and macrophage function. For this, I analyse the effects of genetic variation on the phenotype and the transcriptome of iPSC-derived microglia, using single cell eQTL and phenotypic QTL analysis and CRISPR screens. During my DPhil I studied the role of islet development in type 2 diabetes (T2D) susceptibility, performing genomics analyses (RNA-seq, ATAC-seq, methylation, ChIP-seq) in an iPSC-derived model of pancreatic beta cells.