This repository contains scripts to recreate the analyses and figures in the study "Transcriptomic profiling of paired primary tumour and omental metastases in High-Grade Serous Ovarian Carcinoma highlights site-dependent expression patterns and neoadjuvant chemotherapy-associated changes" Vanagas et al. 2026. Part of the Advanced Cancer Biology Course, Faculty of Medicine, Lund University, Sweden.
This repository is divided into 3 parts.
- Initial analyses.
- Metastasis vs Primary analyses.
- Neoadjuvant vs treatment naive analyses.
Part 1: Contains scripts for general data overview (Tumour purity estimation, PCA, variancePartition and plotting downloaded cibersort results). Script 1.1 should be run to calculate tumour purity scores which are then appended to the sample metadata for downstream scripts.
Part 2: Contains scripts for Metastasis vs Primary analyses. Scripts 2.1-2.4 should be ran in order. 2.5 and 2.6 can be ran independetly.
Part 3: Contains scripts for Neoadjuvant vs treatment naive analyses. Run in order.
Request to access metadata and the counts matrix should be emailed to Prof. Ingrid Hedenfalk at ingrid.hedenfalk@med.lu.se