autoprot

autoprot simplifies analysis of quantitative mass spectrometry-based proteomics data processed with MaxQuant by integrating Python and R algorithms and generating interactive visualizations.

Key Features:

• Cross-language integration: Provides access to established statistical testing and data transformation functions written in both Python and R.
• Interactive visualization: Generates JavaScript-based interactive plots that can be integrated into interactive web applications.
• Jupyter compatibility: Functions as a Jupyter-compatible analysis pipeline for exploratory research and result communication.
• Customizable pipelines: Offers standardized, fast and reliable analysis while maintaining high customizability to tailor pipelines to specific experiments.

Scientific Applications:

• Quantitative proteomics analysis: Processes and analyzes complex quantitative mass spectrometry-based proteomics datasets through standardized pipelines.
• Statistical testing: Performs statistical analysis on MaxQuant-processed proteomics data using established Python and R functions.
• Data transformation: Applies data transformation methods to proteomics datasets as part of analysis workflows.
• Exploratory data analysis: Facilitates interactive data exploration and visualization for hypothesis generation and result interpretation.

Methodology:

autoprot is implemented in Python ≥ 3.9 and processes MaxQuant output through integrated Python and R algorithms for statistical testing and data transformation, with JavaScript-based interactive plot generation.