Changelog

All notable changes to ProteoPy will be documented in this file. The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

  • Tutorials: Protein-level analysis notebook

[0.1.0] - 2025-01-29

Initial release of ProteoPy.

Added

  • Data import (pr.read): Support for DIA-NN and generic long-format tables

  • Annotation (pr.ann): Functions to annotate samples (.obs) and variables (.var)

  • Quality control (pr.pp): Completeness filtering, CV calculation, contaminant removal

  • Preprocessing (pr.pp): Median normalization, downshift imputation

  • Differential abundance (pr.tl): t-test, Welch’s test, ANOVA with multiple testing correction

  • Proteoform inference (pr.tl): COPF algorithm reimplementation for detecting functional proteoform groups

  • Visualization (pr.pl): Volcano plots, abundance rank plots, intensity distributions, CV plots, correlation matrices, hierarchical clustering profiles

  • Datasets (pr.datasets): Built-in example datasets (Karayel 2020)