DIAToolComp

DIATool — Unified DIA Proteomics Data Converter

Welcome to DIATool! This tool simplifies the comparison and integration of results from different Data-Independent Acquisition (DIA) proteomics software by converting their output into a standardized format.

We support conversion from popular DIA analysis platforms including:

• EncyclopeDIA
• DIA-NN
• Skyline
• OpenSWATH
• Spectronaut

Whether you're benchmarking tools, performing meta-analyses, or building downstream pipelines, DIATool ensures your data speaks the same language. 🧬📊

🔗 Try it live: https://www.guomics.com/DIAtool/

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📁 Repository Overview

• app.R
  The core Shiny web application that powers the interactive interface. It handles file uploads, format detection, data conversion, and result downloads.

• template.RData
  A sample dataset used internally by the app for demonstration and testing purposes. It includes example matrices in the unified format to illustrate expected outputs.

• ReportConversion/
  Contains backend conversion scripts and logic for parsing and standardizing outputs from each supported DIA tool.

• ResultPlot/
  Utilities for visualizing converted results (e.g., QC metrics, overlap plots)—used in the online version for exploratory analysis.

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🚀 How It Works

1. Upload your result file(s) from any supported DIA software.
2. DIATool automatically detects the source tool and converts the data into a consistent tabular format at three levels:
   • Precursor
   • Peptide
   • Protein
3. Download the standardized matrices for downstream analysis or cross-tool comparison.

This unified schema enables seamless integration with statistical tools, visualization libraries, or machine learning workflows.

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💻 Run Locally (Optional)

To run the app on your own machine:

# Install required packages (if needed)
install.packages(c("shiny", "dplyr", "readr", "stringr"))

# Clone the repo
git clone https://github.com/guomics-lab/DIAToolComp.git
cd DIAToolComp

# Launch the app
Rscript -e "shiny::runApp()"