Analysis code for "A cellular atlas of the healthy human adult female urethra"

Overview

This repository contains the code necessary to replicate the analysis carried out in the above listed manuscript.

Usage

1. Clone this repo and change into the directory.
2. Launch R. If renv is not installed, it will be bootstrapped.
3. Prepare the R analysis environment by running renv::restore().
4. Acquire the raw data (fastq files).
5. Run Cell Ranger Count with version and parameters matching run_cellranger_count.slurm.
6. Run CellBender with the image version and parameters matching run_cellbender.slurm.
7. (Optional) Install the cellbender conda environment matching environment_cellbender.yml, and run calc_rho_from_cellbender.slurm to calculate contamination fractions.
8. Run 01_initial_analysis.R, modifying the input and output lines as necessary.
9. Run 02_preprocess.R, modifying the input and output lines as necessary.
10. Run 03_lineage_filtering.R, modifying the input and output lines as necessary.