autoprot

Welcome to the documentation of the autoprot package.

Autoprot is a Python module for simplified analysis of quantitative mass spectrometry-based proteomics experiments processed with the MaxQuant software. It provides access to established functions written in both Python and R for statistical testing and data transformation. Moreover, it generates JavaScript-based interactive plots (based on the plotly library) that can be integrated into interactive web applications. Thereby, autoprot offers standardised, fast and reliable proteomics data analysis while maintaining the high customisability required to tailor the analysis pipeline to specific experiment

How to install

For more information on how to install the package.

• Installation
• Downloading autoprot
• Troubleshooting

The main package

The autoprot package is divided into three main parts: preprocessing, analysis and visualization.

Preprocessing module

The preprocessing module is used to preprocess the protein sequences.

• Preprocessing
  • Transformations
  • Normalization
  • Imputation
  • Filtering
  • Data handling
  • Seqeunce annotation for data preprocessing

Analysis module

The analysis module is used to analyze the protein sequences.

• Analysis
  • Clustering
  • Functional Annotation
  • Principal Component Analysis
  • Quality Control
  • Statistical Tests
  • Various Statistical Tools

Visualization module

The visualization module is used to visualize the results of the analysis.

• Visualization
  • Annotation
  • Basic visualization functions
  • Visualization of Quality Control Metrics