Proteomics Data Analysis Python Packages

sdrf-pipelines

SDRF official validator and converts SDRF to pipeline configuration files

alphapepttools

Search- and quantification-engine agnostic biological interpretation of proteomics data

fulcrum-ms

Fulcrum Pipeline: extreme-scale proteomics processing engine from Seer

spectrum-io

IO related functionalities for oktoberfest.

proffer

Fast and flexible tool for protein inference

proteomicscopylot

Proteomics CoPYlot: an open-source analysis and visualization tool for proteomics data, with quality control, statistics, phosphoproteomics, and reproducible Python/R workflows.

proteoannot

Standalone Python package for annotating protein sequences with biological and physicochemical properties (iFeature, IEDB, SignalP) for reverse vaccinology. Extracted from VacSol-ML(ESKAPE); supports multi-allele MHC-I/II epitope prediction. Provides both a Python API and a CLI

xomics

Python framework for explainable omics analysis