Spatiotemporal-multimodal integration reveals a BCG-induced skin-blood crosstalk

reproduce all analyses using this codebase

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Table of Contents

• Overview
• Getting Started
• Running the Scripts
• How to Cite

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Overview

This repository contains scripts for data exploration, differential expression analysis, and multi-modal data integration. The project uses R and R Markdown to process, analyze, and visualize results from diverse data sources, including cfRNA, dermatological images, and GeoMx spatial transcriptomics data.

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Getting Started

1) clone repo

git clone https://github.com/CompBio-Lab/bcg_skinblood_crosstalk.git

2) get data

download data from this zenodo link put data in bcg_skinblood_crosstalk folder

3) open .Rproj file

bcg_skinblood_crosstalk.Rproj

4) Install renv if you don't have it:

install.packages("renv")

5) Restore the project environment from renv.lock:

renv::restore()

This will install the exact package versions used when this project was last saved.

Running scripts

• Open .Rmd files in RStudio

• Knit the files to HTML or run interactively

• Explore the folder structure above to locate analyses of interest

How to Cite

• preprint