Master Thesis

This is the code from the Master thesis "Differential expression and TCR repertoire analysis by RNAseq of CD4+ and CD8+ T cells during immunotherapy for B-cell lymphoma" submitted by Andoni Sáenz Sala in the Master in Computational Methods in Science at the School of Sciences of the University of Navarra. August 2023.

This repository contains all the code implemented in my project.

1. The file Main_script.R contains all the code implemented in the RNAseq analysis pipeline, including:

   • All libraries that were used in the project.
   • Reference genome indexing and reads alignment.
   • Generation of a counts matrix.
   • Data pre-processing and filtering steps.
   • Differential Expression Analysis with DESeq2.
   • Data normalization methods and visualization.
   • Obtention of differentially expressed gene lists.
   • Functional analysis with ORA and GSEA.

2. The file TCR_analysis.R contains all the code implemented in the TCR clonality analysis pipeline, including:

   • Extraction of TCR clonal repertoire information with MiXCR (this part was executed in the Windows Powershell, not in R).
   • TCR clonotype analysis and visualization with immunarch.
   • Analysis of TCR clonal repertoire diversity.

3. The file MultiQC_analysis.R contains all the code implemented to generate plots for the outputs of the quality control analysis with MultiQC.