zekaihuang-pku / hgsoc_tme_heterogeneity

Analysis of treatment naive and neo-adjuvant chemotherapy treated high-grade serous ovarian cancer samples

Unraveling tumor–immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy

This repository contains the scripts for data processing, analysis and figure generation using bulk mRNA microarray data, whole exome sequencing, and imaging data integration of high-grade serous ovarian cancer human samples pre- and post-neoadjuvant therapy.

Tha paper can be found at:

Unraveling Tumor-Immune Heterogeneity in Advanced Ovarian Cancer Uncovers Immunogenic Effect of Chemotherapy

Raw data

Microarray mRNA data can be found at GEO: GSE146965

Whole Exome Sequencing data, TCR sequencing data, and imaging data have to be requested to [email protected].

Repository

Scripts, Data, and, Figures are organized per figure in the manuscript.

The packages needed to execute the scripts can be found in conda_env.yml.

Preprocessed microarray mRNA data files are already provided in the Data folder 1.