This repository manages the code to analyze the results of drug screens in cNF organoids together with omics measurements of the tumor data.
The data for this code is hosted on Synapse at http://synapse.org/cnfDrugResponse
We are collecting omics measurements from cNF organoid samples together with drug response data to identify potential biomarkers of drug response.
The current analysis workflow (see analysis/) is organized as a small set of notebooks that:
- Join batches and (when needed) batch-correct RNA, global proteomics, and phosphoproteomics (via ComBat), and generate basic QC plots (e.g., PCA).
- Summarize drug response behavior across the cohort (most efficacious / most variable drugs + a cohort-wide drug heatmap).
- Correlate drug response with molecular features per modality (Spearman correlations + FDR), producing per-drug summaries of correlated features.
- Perform pathway enrichment on correlated features (direction-aware enrichment with leapR) to interpret putative mechanisms and biomarkers.