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108 repositories

peptide-gnn
Public
A graph-based deep learning model for predicting and explaining peptide LC-RT data.
Python
•
MIT License
•0•0•0•0•Updated May 5, 2026May 5, 2026
mzdata-converter
Public
Bruker and Thermo raw file to mzML converter built with mzdata.
Rust
•
Apache License 2.0
•0•0•0•0•Updated Apr 28, 2026Apr 28, 2026
MuMDIA
Public
Jupyter Notebook
•
Apache License 2.0
•0•3•8•1•Updated Apr 24, 2026Apr 24, 2026
DeepLC
Public
DeepLC: Retention time prediction for peptides carrying any modification.
deep-learning proteomics peptides
deep-learning proteomics peptides retention-time peptide-modification
Python
•
Apache License 2.0
•24•75•0•1•Updated Apr 24, 2026Apr 24, 2026
ms2pip
Public
MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
machine-learning proteomics mass-spectrometry
machine-learning proteomics mass-spectrometry peptide-identification spectrum-prediction peptide-spectrum
HTML
•
Apache License 2.0
•19•49•6•0•Updated Apr 22, 2026Apr 22, 2026
ms2rescore-rs
Public
Rust functionality for the MS²Rescore package
Rust
•
Apache License 2.0
•4•2•0•1•Updated Apr 15, 2026Apr 15, 2026
IM2Deep
Public
Collisional cross-section prediction for modified and multiconformational peptides
proteomics mass-spectrometry peptides
proteomics mass-spectrometry peptides ion-mobility collisional-cross-section timstof
Python
•
Apache License 2.0
•2•13•0•0•Updated Apr 14, 2026Apr 14, 2026
compomics-utilities
Public
Open source Java library for computational proteomics
bioinformatics proteomics computational-proteomics
bioinformatics proteomics computational-proteomics
Java
•17•35•8•0•Updated Apr 12, 2026Apr 12, 2026
omssa-parser
Public
Java based parser for OMSSA OMX files
bioinformatics proteomics omssa
bioinformatics proteomics omssa
Java
•0•0•0•0•Updated Apr 12, 2026Apr 12, 2026
ms2rescore
Public
Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
proteomics percolator peptide-identification
proteomics percolator peptide-identification ms2pip deeplc
Python
•
Apache License 2.0
•21•64•14•0•Updated Apr 11, 2026Apr 11, 2026
molcraft
Public
A python package for building powerful molecular graph neural networks for chemistry and biology.
python machine-learning deep-learning
python machine-learning deep-learning tensorflow keras graph-neural-network molecular-machine-learning
Python
•
MIT License
•0•2•0•0•Updated Apr 9, 2026Apr 9, 2026
MoDPAv1.0
Public
MoDPA repository for publication
Jupyter Notebook
•
Apache License 2.0
•0•1•0•0•Updated Apr 7, 2026Apr 7, 2026
pdb-topology-viewer
Public
PDB Topology Viewer
TypeScript
•
Apache License 2.0
•5•0•0•0•Updated Apr 3, 2026Apr 3, 2026
iDeepLC
Public
iDeepLC: A deep Learning-based retention time predictor for unseen modified peptides with a novel encoding system
Python
•
Apache License 2.0
•2•2•0•0•Updated Apr 3, 2026Apr 3, 2026
protean-viz
Public
Tool to visualize user input such as modifications and peptides, including custom input files and search engine input files
JavaScript
•
Apache License 2.0
•0•0•0•0•Updated Apr 2, 2026Apr 2, 2026
peptide-shaker
Public
Interpretation of proteomics identification results
java bioinformatics proteomics
java bioinformatics proteomics protein-identification
Java
•20•54•45•0•Updated Mar 21, 2026Mar 21, 2026
D012554A_2025
Public
Jupyter Notebook
•
Apache License 2.0
•4•2•0•0•Updated Mar 19, 2026Mar 19, 2026
eluflow
Public
A command line tool for training and deploying molecular graph neural networks for chromatography.
Python
•
MIT License
•0•0•0•0•Updated Mar 13, 2026Mar 13, 2026
MSqRobPy
Public
Python implementation of MSqRob2 R package
Python
•
Apache License 2.0
•0•0•0•0•Updated Mar 12, 2026Mar 12, 2026
ThermoRawFileParser
Public
Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono
C#
•
Apache License 2.0
•58•243•13•0•Updated Mar 7, 2026Mar 7, 2026
intro-to-deep-learning
Public
Practical introduction to neural networks with Pytorch and Lightning
tutorial lightning pytorch
tutorial lightning pytorch recurrent-neural-networks neural-networks convolutional-neural-networks
Jupyter Notebook
•
Creative Commons Attribution 4.0 International
•0•2•0•0•Updated Mar 6, 2026Mar 6, 2026
tabloidProteome
Public
HTML
•
Apache License 2.0
•0•1•0•3•Updated Mar 3, 2026Mar 3, 2026
psm_utils
Public
Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
python parsing proteomics
python parsing proteomics mass-spectrometry peptide-identification peptide-spectrum-matches
Python
•
Apache License 2.0
•10•31•10•1•Updated Feb 12, 2026Feb 12, 2026
oui-discovery
Public
Collaboration between CompOmics & OpenProt group
Jupyter Notebook
•
Apache License 2.0
•0•0•0•0•Updated Jan 8, 2026Jan 8, 2026
ecoli-peptideatlas-manuscript
Public
Code used to produce figures in the E. coli PeptideAtlas Paper
Jupyter Notebook
•
Apache License 2.0
•0•1•0•0•Updated Dec 18, 2025Dec 18, 2025
mumble
Public
Finding the perfect modification for your mass shift
Python
•
Apache License 2.0
•1•6•1•2•Updated Dec 3, 2025Dec 3, 2025
lsabd-machine-learning-tutorials
Public
Tutorials machine learning for the Large Scale Analysis of Biomedical Data course
Jupyter Notebook
•
Creative Commons Attribution 4.0 International
•1•0•0•0•Updated Nov 4, 2025Nov 4, 2025
Peptonizer2000
Public
Confidence for taxonomic analysis in metaproteomics. Get ready to peptonize!
Python
•
Apache License 2.0
•0•3•3•0•Updated Nov 3, 2025Nov 3, 2025
lesSDRF
Public
Jupyter Notebook
•
Apache License 2.0
•9•10•3•1•Updated Oct 15, 2025Oct 15, 2025
reporter
Public
Protein quantification based on reporter ions
bioinformatics proteomics protein-quantification
bioinformatics proteomics protein-quantification reporter-ions
Java
•2•4•5•0•Updated Aug 15, 2025Aug 15, 2025

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Computational Omics and Systems Biology Group

All

All

108 repositories

peptide-gnn

mzdata-converter

MuMDIA

DeepLC

ms2pip

ms2rescore-rs

IM2Deep

compomics-utilities

omssa-parser

ms2rescore

molcraft

MoDPAv1.0

pdb-topology-viewer

iDeepLC

protean-viz

peptide-shaker

D012554A_2025

eluflow

MSqRobPy

ThermoRawFileParser

intro-to-deep-learning

tabloidProteome

psm_utils

oui-discovery

ecoli-peptideatlas-manuscript

mumble

lsabd-machine-learning-tutorials

Peptonizer2000

lesSDRF

reporter

All

All

Repositories list

108 repositories