Using cell-specific late-phase asthma mRNA biomarkers to repurpose drugs that concurrently reverse disease signatures across multiple immune cell-types

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 the:

1. identification of blood-based mRNA biomarkers of the late-phase asthmatic response (LAR-mRNA) using the NanoString PanCancer platform
2. enrichment analysis of PanCancer and existing mRNA biomarkers
3. evaluation of LAR-mRNA biomarkers in predicting asthma exacerbations and severity
4. determine cellular specificity of the LAR-mRNA biomarkers
5. identifying drugs that can reverse allergen-induced exprsesion of LAR-mRNA biomarkers

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Getting Started

1) clone repo

git clone https://github.com/CompBio-Lab/asthma_LAR-mRNA_biomarkers.git

2) get data

download data from this zenodo link put data in asthma_LAR-mRNA_biomarkers folder

3) open .Rproj file

asthma_latephase.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 in the src folder

• Knit the files to HTML or run interactively

How to Cite

• Zhang et al., PLOS Computational Biology 2026