moma: molecular markers in rat barrel cortex

This repository contains analyses of the laminar organization of molecularly defined inhibitory neurons (INHs) in rat barrel cortex.

Setup

This project is pure R. We use renv to manage dependencies and ensure reproducibility.

From the root of the repository:

source("setup.R")

This will install any missing R packages required for analysis and testing, load all required packages, and initialize or restore the renv project environment.

Running Analyses

All scripts are in the scripts/ folder:

• step1_GAD67.R – Process GAD67+ INH densities and plot laminar distribution
• step2_scaling_factors.R – Calculate scaling factors for optical sections
• step3_scaled_cortex.R – Process other molecular markers (PV, Sst, Vip) and plot densities
• step4_create_tables.R – Generate summary tables by column and layer

Figures and tables are saved in the results/ folder.

Running Tests

Unit tests are located in the tests/ folder. To run all tests:

library(testthat)
test_dir("tests")