Post-partum breast cancer

This repository contains the code for the analysis of RNA-seq data from the KWF project "Postpartum breast cancer diagnosed during involution: a distinct entity with unique clinicopathological, molecular and immunological features".

Approach

This project utilizes a three-pronged approach:

1. Survival analysis based on clinical outcomes within the PPBC cohort
2. RNAseq-based analyses on FFPE-preserved primary tumors from a subset of patients within the PPBC cohort
3. Spatial analysis from Vectra multiplex panels on a subset of the aforementioned patients

Instructions

1. Install R and Python and their dependencies. R dependency versions are in renv.lock and can be restored with renv::restore(). For Python, use pipenv install to generate a virtual environment based on requirements.txt, and pipenv shell to activate it.
2. Add the RNA fastq files to data/rnaseq/RAW and the spatial vectra files to data/vectra/raw.
3. Run with snakemake. If you get a permission error when knitting a notebook, run snakemake again. This is due to rmarkdown's inability to handle multiple simultaneous knitting jobs from the same file, and should resolve itself on subsequent runs.

Note: to get the figures numbered as they are in the published article, you will need to type snakemake renumber_figs into the console.