Code for "Mechanisms of risk in pregnancy-associated triple negative breast cancer: insights from spatial omics" Veraksa, et al. biorxiv (2026) DOI [10.64898/2026.03.09.710650]
Spatial omics analysis of epithelia and TME in pregnancy-associated triple negative breast cancer identifies mechanisms of risk associated with mammary gland involution and informs future treatment options.
This repository contains R scripts to reproduce all statistical analyses and figures in the paper. Tested using R 4.5. Package versions are noted in the paper Methods.
| Script | Description |
|---|---|
analysis/01_PABC_QC.R |
Data quality control and preprocessing; UMAPs |
analysis/02_PABC_DEGs.R |
Differential expression analysis |
analysis/03_PABC_Enrichment.R |
Functional enrichment of differential results |
analysis/04_PABC_TF_Targets.R |
Transcription factor target analysis |
analysis/05_PABC_Deconvolution.R |
Cell type deconvolution of TME |
analysis/06_PABC_CellState.R |
Cell state identification in TME |
analysis/07_PABC_Pseudotime.R |
Pseudotime analysis in post-involution samples |
analysis/08_PABC_BulkSignalR.R |
Ligand-receptor interaction inference |
plotting/Main_Figures_Plotting.R |
Main paper figures |
plotting/Supplemental_Figures_Plotting.R |
Supplemental paper figures |
Raw GeoMx data and post-QC data object are available in GEO: GSEXXXXXX
Darya Veraksa - dveraksa@ucsd.edu