The codebase of the OpenMS project

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

A collection of Galaxy-related training material

A Python API for the RCSB Protein Data Bank (PDB)

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

Proteomics search & quantification so fast that it feels like magic

Various teaching material

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data

A modular, python-based framework for mass spectrometry. Powered by nbdev.

Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)

sensitive and precise assembly of short sequencing reads

Base Classes and Functions for Mass Spectrometry and Proteomics

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

Deep learning framework for proteomics

A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

Olink R package: A collection of functions to facilitate analysis of proteomic data from Olink. The goal of this package is to help users extract biological insights from proteomic data run on the Olink platform.

The Proteomics Experimental Design file format: Standard for experimental design annotation

An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.