A set of ready to use Agent Skills for research, science, engineering, analysis, finance and writing.

🧬 gget enables efficient querying of genomic reference databases

The codebase of the OpenMS project

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

A collection of Galaxy-related training material

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

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

A cross-platform proteomics data analysis suite

Proteomics search & quantification so fast that it feels like magic

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

Various teaching material

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

sensitive and precise assembly of short sequencing reads

Deep learning framework for proteomics

Base Classes and Functions for Mass Spectrometry and Proteomics

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

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.

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

modular & open DIA search

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

The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets

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

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

A deep learning toolkit for mass spectrometry

Python Package for the downstream analysis of mass-spectrometry-based proteomics data

Toolbox for including enzyme constraints on a genome-scale model.

Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.

DeepLC: Retention time prediction for peptides carrying any modification.

Exon is an OLAP query engine specifically for biology and life science applications.

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.