Welcome to alphapeptstats’s documentation!

AlphaPeptStats is an open-source package for analyzing mass spectrometry-based proteomics data.

AlphaPeptStats was developed to in order to simplify and standardize the process of analyzig complex datasets. Hereby AlphaPeptStats supports proteomics data generated by AlphaPept, DIA-NN, FragPipe and MaxQuant. The tool allows a structured workflow like importing data, preprocessing data and visualization.

Contents:

• Installation
  • Pip
• Data import
  • Importing data from a Proteomics software
  • Preparing metadata
  • Creating a DataSet
• Data preprocessing
  • Removal of contaminations
  • Normalization
  • Imputation
  • Subset Data
  • Remove Samples
• Functions
  • Preprocessing
  • Figures
  • Statistical Analysis
  • GO Analysis
  • Misc
• Workflow Example
• GO Analysis
  • Requirements
• API
  • File Loader
  • DataSet

Indices and tables

• Index

• Module Index

• Search Page