RNAseq_DESeq2_Airway_example

This repository contains a reproducible RNA-seq differential expression analysis pipeline using the Bioconductor airway dataset as an example.

Contents

• run_analysis_and_prepare_repo.R: main R script (this file).
• results/: CSV outputs (DE results and normalized counts).
• figures/: PNG figures (PCA, Volcano, Heatmap).

How to run

1. Open this project in RStudio.
2. Run source('run_analysis_and_prepare_repo.R').
3. Review files in results/ and figures/.

Notes

• This example uses the Bioconductor airway dataset so the pipeline runs without needing to download raw FASTQ files.
• To analyze your own Salmon/Kallisto output, replace the data-loading section with tximport code that imports your quant.sf files.

Citation

If you use this pipeline, please cite the relevant packages (DESeq2, etc.).