Scripts for: Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction

Description

This record includes scripts to reproduce the WGS and RNA-seq analysis as part of the study “Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction" by Chen et al., 2022. All scripts are available with a Creative Commons Attribution 4.0 International License (CC BY 4.0: http://creativecommons.org/licenses/by/4.0/).

WGS scripts

This script collection includes scripts to reproduce the WGS analysis as part of the study by Chen et al., 2022. It processes the outputs from Strelka/Mutect2 for somatic SNV calling and from Control-FREEC for somatic Copy Number Alteration (CNA) calling. Inputs the results of the somatic SNV and CNA calling, and outputs several informative plots. Further details are available in the Materials & Methods part of Chen et al., 2022 and in the corresponding README file.

RNA-seq R project

This script collection includes scripts to reproduce the RNA-seq analysis as part of the study by Chen et al., 2022. It is bundled as an R project. It performs quality control of the ex-vivo model of breast cancer, analyses 4OHT/NDT induced changes, and explores individual patients (as model for precision/personalized medicine). Inputs the RNA-seq gene count data and the patient clinical data, and outputs several informative plots. Further details are available in the Materials & Methods part of Chen et al., 2022 and in the corresponding README file.