Pompe Transcriptomics – GSE38680

This repository hosts a reproducible R workflow for analysing the Infantile-Onset Pompe Disease (IOPD) dataset GSE38680 generated on the Affymetrix U133 Plus 2.0 platform. The analysis covers normalisation, differential expression, functional enrichment, miRNA integration and PPI network exploration.

Quick start

# 1) set up environment
conda env create -f environment/environment.yml
conda activate pompe

# 2) obtain data
# CEL files and `pheno.csv` are tracked via Git LFS under `metadata/`
git lfs install
git lfs pull

# 3) run analysis
Rscript microarray_analysis_pompe.R

Results and plots are written to the results/ directory.

Project structure

• microarray_analysis_pompe.R – main R script
• config/ – samplesheet.csv and params.yaml
• metadata/ – CEL files and phenotype table (LFS)
• environment/ – Conda environment specification
• docs/ – additional documentation such as methods

Data and ethics

All input data originate from the public GEO accession GSE38680. No personal health information is included.

Data via Git LFS

After cloning: git lfs install git lfs pull

Citation

Please cite:

Tosun F., Bayrak H. 2025. Transcriptomic and Functional Analysis of Pompe Disease.

See CITATION.cff for machine‑readable metadata.