MagmaFlow_v10.0.1: Interactive Volcano Plot Application

# 📊 MagmaFlow: Interactive Volcano Plot Application (v10.0.1) MagmaFlow is a **JavaFX-based scientific visualization tool** for creating **publication-ready volcano plots**.It enables researchers to **explore, annotate, and export** differential expression results interactively, ensuring high-quality figures for papers, presentations, and data exploration. --- ## 🚀 Features - Interactive volcano plot exploration- Drag-and-drop gene annotation with labels- Customizable thresholds (log2FC, p-value, adjusted p-value)- Export-ready plots (PNG, SVG, PDF)- Persistent project save/load (JSON format)- Publication-quality styling with white backgrounds and clean legends- Cross-platform (Windows, macOS, Linux) --- ## 🛠 Installation ### 🔹 Download The latest release is available here:👉 [MagmaFlow Releases on GitHub](https://github.com/carlosbuss1/MagmaFlow/releases/tag/magmaflow) ### 🔹 Windows / Linux - Download the `.jar` file.- Run with: ```bashjava -jar MagmaFlow-x.y.z.jar 🔹 **macOS** 1. Download the `.dmg` installer from the [Release page](https://github.com/yourusername/MagmaFlow/releases).2. Open the downloaded `.dmg` file and drag the **MagmaFlow** icon into your **Applications** folder.3. Try launching the app. If macOS blocks it: * Go to **System Settings** → **Privacy & Security** → **Security** * Scroll down to **"Allow accessories to connect"** * Click **"Allow"** to approve MagmaFlow * Then re-open the app > *This step is needed because macOS sometimes restricts apps from unidentified developers.* --- 📂 **Usage** * No pre-manipulation of data is required. You can use the direct output from your DEA (RNA-seq, proteomics, or phosphoproteomics).* Import your results (CSV/TSV).* The app automatically recognizes the required columns: * `Gene` * `log2FC` * `p-value` * `adj-pvalue` (optional but recommended)* Adjust thresholds for log2 fold-change and p-value.* Explore interactively: click on points to annotate genes.* Export figures for your manuscript. **Example input format:** | Gene | log2FC | p-value | adj-pvalue || :------ | :----: | :-----: | :--------: || PTPRF | 1.2 | 0.004 | 0.007 || PTPN12 | -0.8 | 0.012 | 0.025 | --- 📖 **Citation** If you use MagmaFlow in your research, please cite: > Carlos Eduardo Buss. MagmaFlow: Interactive Volcano Plot Application. Signal Transduction and Metabolism Laboratory (STML), Free University of Brussels (ULB). DOI: 10.5281/zenodo.17011630 A `CITATION.cff` file is included for GitHub’s citation support. --- 📜 **License** MagmaFlow is distributed under the GNU General Public License v3 (GPL-3.0) with additional terms: * Utilization of this software (in whole or in part) for scientific or academic purposes must be accompanied by an appropriate citation of the original authors and DOI.* Commercial use of this software, or any derivative work, is not permitted without prior written consent from the copyright holder. See the full [LICENSE](https://github.com/yourusername/MagmaFlow/blob/main/LICENSE) file for details. --- 👨‍💻 **Author** **Carlos Eduardo Buss** Senior Bioinformatician, Signal Transduction and Metabolism Laboratory (STML), Free University of Brussels (ULB) 📧 [[email protected]](mailto:[email protected])