ProteoPy

ProteoPy streamlines protein- and peptide-level quantitative proteomics analysis by using the AnnData class as its core data structure to preserve all metadata within a single object.

Key Features:

• Data Import and Preprocessing: ProteoPy streamlines data import and preprocessing for quantitative proteomics data.
• Differential Analysis: ProteoPy performs differential analysis on protein- and peptide-level data.
• Proteoform Group Inference: A reimplementation of the COPF algorithm enables proteoform group inference directly from peptide-level data, facilitating identification of proteoform-specific regulation and isoform usage.
• Ecosystem Integration: ProteoPy integrates with the scanpy and muon ecosystems for multi-omics analysis.

Scientific Applications:

• Quantitative Proteomics Analysis: ProteoPy supports protein- and peptide-level quantitative proteomics analysis.
• Proteoform-Specific Regulation: ProteoPy enables identification of proteoform-specific regulation and isoform usage through proteoform group inference from peptide-level data.
• Multi-Omics Analysis: ProteoPy supports reproducible and scalable multi-omics analysis through integration with scanpy and muon.

Methodology:

ProteoPy is built around the AnnData class as its core data structure. It reimplements the COPF algorithm for proteoform group inference directly from peptide-level data.