OmicsCheck: Intelligent Quality Assessment for Gene Expression Data
OmicsCheck is a cutting-edge, automated tool designed to evaluate the quality of gene expression datasets from GEO (Gene Expression Omnibus). It intelligently analyzes raw expression matrices and generates professional PDF reports, visual summaries, and interpretable quality metrics – enabling researchers to screen studies before conducting downstream analysis.
Features
- Download and parse GEO Series Matrix files automatically.
- Auto-orientation of matrices (genes × samples vs. samples × genes).
- Log2 transformation suggestions based on data distribution.
- Data filtering for the most variable genes (top-N).
- QA Score Evaluation using multi-criteria assessment.
- PCA and Heatmap visualization of gene-level variability.
- PDF report generation with visual plots and summary stats.
- Exports analysis files in
.jsonand.csvformats.
Installation
pip install omicscheck
Requires Python 3.8+
Usage
omicscheck run GSE12345
This will:
- Download the matrix file for
GSE12345 - Parse and analyze the data
- Evaluate quality and suggest improvements
- Generate visual plots
- Create a full PDF report at:
~/Desktop/OmicsCheck/GSE12345/report.pdf
Quality Evaluation Logic
OmicsCheck uses a composite QA Score based on:
- Matrix completeness
- Distribution characteristics
- Gene variance
- Sample PCA spread
Each dataset receives a final Rating: Excellent, Good, Moderate, or Poor
Output Files
report.pdf: Professional scientific reportanalysis.json: Full results in machine-readable formatanalysis.csv: Simplified metrics tableboxplot.png,heatmap.png,pca_plot.png: Generated plots
Example Output
Example report: docs/report_example.pdf
OmicsCheck
A smart pre-download screening tool for high-quality omics datasets.
Citation
Ahmed Yassin. OmicsCheck Enables Improved Selection of High-Quality Gene Expression Datasets: A Pre-download Screening Tool with Biological Impact Assessment.
Research Square (2025).
https://doi.org/10.21203/rs.3.rs-7297713/v1
Contributing
We welcome contributions! Fork the repo and submit a pull request.
Contact
Lead Developer: [AHMED YASSIN || Computational Biologist]
Email: [Ahmedyassin300@outlook.com]
Project Page: [https://github.com/AHMEDY3DGENOME/OmicsCheck]
© 2025 OmicsCheck Team. All rights reserved.
1 maintainer
Metadata
1 maintainer
Release files for omicscheck 1.0.2
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