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Computational Omics and Systems Biology Group

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101 repositories

molcraft
Public
Deep learning on molecules: Minimalistic and powerful implementations of molecular graphs and graph neural networks.
python machine-learning deep-learning tensorflow keras graph-neural-network molecular-machine-learning
Python
•
MIT License
•0•1•0•0•Updated Dec 11, 2025Dec 11, 2025
DeepLC
Public
DeepLC: Retention time prediction for peptides carrying any modification.
deep-learning proteomics peptides retention-time peptide-modification
Python
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Apache License 2.0
•24•72•0•1•Updated Dec 10, 2025Dec 10, 2025
ms2pip
Public
MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
machine-learning proteomics mass-spectrometry peptide-identification spectrum-prediction peptide-spectrum
HTML
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Apache License 2.0
•19•47•7•4•Updated Dec 10, 2025Dec 10, 2025
ecoli-peptideatlas-manuscript
Public
Code used to produce figures in the E. coli PeptideAtlas Paper
Jupyter Notebook
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Apache License 2.0
•0•1•0•0•Updated Dec 3, 2025Dec 3, 2025
ms2rescore
Public
Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
proteomics percolator peptide-identification ms2pip deeplc
Python
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Apache License 2.0
•20•62•22•2•Updated Dec 3, 2025Dec 3, 2025
mumble
Public
Finding the perfect modification for your mass shift
Python
•
Apache License 2.0
•1•5•1•2•Updated Dec 3, 2025Dec 3, 2025
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 Dec 2, 2025Dec 2, 2025
oui-discovery
Public
Collaboration between CompOmics & OpenProt group
Jupyter Notebook
•
Apache License 2.0
•0•0•0•0•Updated Dec 1, 2025Dec 1, 2025
peptide-shaker
Public
Interpretation of proteomics identification results
java bioinformatics proteomics protein-identification
Java
•18•53•45•0•Updated Nov 26, 2025Nov 26, 2025
lsabd-machine-learning-tutorials
Public
Tutorials machine learning for the Large Scale Analysis of Biomedical Data course
Jupyter Notebook
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Creative Commons Attribution 4.0 International
•0•0•0•0•Updated Nov 4, 2025Nov 4, 2025
ms2rescore-rs
Public
Rust functionality for the MS²Rescore package
Rust
•
Apache License 2.0
•4•2•0•1•Updated Nov 4, 2025Nov 4, 2025
Peptonizer2000
Public
Confidence for taxonomic analysis in metaproteomics. Get ready to peptonize!
Python
•
Apache License 2.0
•0•1•3•0•Updated Nov 3, 2025Nov 3, 2025
tabloidProteome
Public
HTML
•
Apache License 2.0
•0•1•0•3•Updated Nov 1, 2025Nov 1, 2025
iDeepLC
Public
iDeepLC: A deep Learning-based retention time predictor for unseen modified peptides with a novel encoding system
Python
•
Apache License 2.0
•1•1•0•0•Updated Oct 29, 2025Oct 29, 2025
psm_utils
Public
Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
python parsing proteomics mass-spectrometry peptide-identification peptide-spectrum-matches
Python
•
Apache License 2.0
•10•29•8•1•Updated Oct 28, 2025Oct 28, 2025
ThermoRawFileParser
Public
Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono
C#
•
Apache License 2.0
•55•231•10•0•Updated Oct 27, 2025Oct 27, 2025
MuMDIA
Public
Jupyter Notebook
•
Apache License 2.0
•0•2•17•1•Updated Oct 24, 2025Oct 24, 2025
lesSDRF
Public
Jupyter Notebook
•
Apache License 2.0
•9•7•3•1•Updated Oct 15, 2025Oct 15, 2025
reporter
Public
Protein quantification based on reporter ions
bioinformatics proteomics protein-quantification reporter-ions
Java
•2•4•5•0•Updated Aug 15, 2025Aug 15, 2025
searchgui
Public
Highly adaptable common interface for proteomics search and de novo engines
java bioinformatics proteomics protein-identification
Java
•15•46•17•0•Updated Aug 15, 2025Aug 15, 2025
compomics-utilities
Public
Open source Java library for computational proteomics
bioinformatics proteomics computational-proteomics
Java
•16•34•8•0•Updated Aug 15, 2025Aug 15, 2025
IM2Deep
Public
Collisional cross-section prediction for modified and multiconformational peptides
proteomics mass-spectrometry peptides ion-mobility collisional-cross-section timstof
Python
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Apache License 2.0
•2•13•0•0•Updated Aug 8, 2025Aug 8, 2025
EUPA_2025_DIA
Public
Analysis of limitations of DIA data analysis for EuPA 2025 presentation
Jupyter Notebook
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Apache License 2.0
•1•0•0•0•Updated Jun 16, 2025Jun 16, 2025
intro-to-deep-learning
Public
Practical introduction to neural networks with Pytorch and Lightning
tutorial lightning pytorch recurrent-neural-networks neural-networks convolutional-neural-networks
Jupyter Notebook
•
Creative Commons Attribution 4.0 International
•0•1•0•0•Updated May 20, 2025May 20, 2025
compomics.github.io
Public
Compomics github website.
SCSS
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MIT License
•1•0•0•0•Updated May 15, 2025May 15, 2025
bioconda-recipes
Public
Conda recipes for the bioconda channel.
Shell
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MIT License
•3.7k•0•0•0•Updated May 8, 2025May 8, 2025
compomics-rover
Public archive
A tool to visualize and validate quantitative proteomics data from different sources.
Java
•0•0•2•0•Updated May 8, 2025May 8, 2025
Workshop_Grenoble_2025
Public archive
Workshop on MS²Rescore for data-driven peptide identification rescoring (Grenoble, 2025)
Jupyter Notebook
•
Apache License 2.0
•0•0•0•0•Updated Apr 2, 2025Apr 2, 2025
molexpress
Public
Graph Neural Networks with Keras 3
Python
•
MIT License
•1•0•0•1•Updated Jan 31, 2025Jan 31, 2025
ML-course-VIB-2024
Public archive
Jupyter Notebook
•51•10•0•0•Updated Nov 26, 2024Nov 26, 2024