Hanlin Zhou: Revealing the alterations of the compositions and molecular features in breast cancer treated with Neoadjuvant chemotherapy by single cell RNA sequencing Date: 01-06-2021    Supervisor: Karsten Kristiansen

In this thesis, I performed single cell transcriptome sequencing of tumor tissues and peripheral blood mononuclear cells (PBMCs) collected from breast cancer patients, in order to dissect the tumor microenviroment (TME) of primary human breast tumor tissues and further characterize the dynamic alterations of peripheral and tumor-infiltrating immune cells during neoadjuvant chemotherapy (NAC). In the analysis process of single cell RNA sequencing data, the problem of doublet removal is a key step. For this reason, I have developed a new and more effective tool to identify doublets, which is named Chord as an open source R package. For interactive analysis and visualization of single cell expression data across conditions, I present Piave based on a shiny framework which does not require users to have programming skills to facilitate in-depth analysis and sophisticated visualization.