Master Thesis

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.