proteogenomics 0.1.0

A CLI tool for proteogenomics analysis

Proteogenomics Prototype

A CLI-based tool for integrating proteomics and genomics data for biomarker identification.

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📌 Features

✔ Supports multiple input formats: FASTA, mzML, CSV, TSV, FASTQ, BAM, VCF, JSON, XML. ✔ Automated data parsing, integration, and biomarker identification. ✔ Mutation-based biomarker detection. ✔ Interactive visualization for analysis. ✔ Fully CLI-based and runs on Linux (Ubuntu).

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📥 Installation

To install the tool from GitHub:

git clone https://github.com/sethuakasanji/Proteogenomics-Prototype.git cd Proteogenomics-Prototype pip install -r requirements.txt

Or install it as a package (after packaging it):

pip install .

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🚀 Usage

To run the CLI:

proteogenomics --help

🔹 Example Commands:

Input Data Processing:

proteogenomics --proteomics /path/to/proteomics_file --genomics /path/to/genomics_file

Mutation-Based Biomarker Detection:

proteogenomics --mutation-detection

View Available Commands:

proteogenomics --help

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🛠 Configuration

Ensure Python 3.8+ is installed.

Works on Linux (Ubuntu).

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📖 Contributing

If you’d like to contribute, fork the repository and create a pull request!

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📞 Contact : [phone] Email : [e-mail]

For queries or issues, reach out via GitHub Issues.