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114 repositories

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
•26•79•1•2•Updated Aug 4, 2026Aug 4, 2026
eluflow
Public
A python package for building powerful transformer models for SMILES.
machine-learning deep-learning keras
machine-learning deep-learning keras transformer smiles
Python
•
MIT License
•0•0•0•0•Updated Aug 4, 2026Aug 4, 2026
MuMDIA
Public
Clean-room Rust reimplementation of MuMDIA, a data-independent-acquisition (DIA) proteomics search engine.
rust bioinformatics proteomics
rust bioinformatics proteomics dia mass-spectrometry
Rust
•
Apache License 2.0
•0•4•0•0•Updated Aug 4, 2026Aug 4, 2026
peptide-shaker
Public
Interpretation of proteomics identification results
java bioinformatics proteomics
java bioinformatics proteomics protein-identification
Java
•21•55•48•1•Updated Aug 1, 2026Aug 1, 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
•23•67•14•1•Updated Aug 1, 2026Aug 1, 2026
bioconda-recipes
Public
Conda recipes for the bioconda channel.
Shell
•
MIT License
•4k•0•0•0•Updated Jul 30, 2026Jul 30, 2026
SCI
Public
Defining Quality Control Standards for Single-Cell Proteomics by Inter-Laboratory Benchmarking
Jupyter Notebook
•
Apache License 2.0
•0•2•0•0•Updated Jul 28, 2026Jul 28, 2026
ms2rescore-rs
Public
Rust functionality for the MS²Rescore package
Rust
•
Apache License 2.0
•4•2•0•1•Updated Jul 25, 2026Jul 25, 2026
CALLC3
Public
A command-line interface tool for training context-aware graph neural networks for chromatography.
Python
•
MIT License
•0•0•0•0•Updated Jul 17, 2026Jul 17, 2026
ristretto
Public
Lean and fast PSM rescoring
Python
•
Apache License 2.0
•0•2•0•0•Updated Jul 16, 2026Jul 16, 2026
molcraft
Public
A python package for building powerful GNN models for molecules.
machine-learning deep-learning keras
machine-learning deep-learning keras molecules graph-neural-network
Python
•
MIT License
•0•2•0•0•Updated Jul 16, 2026Jul 16, 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•14•0•0•Updated Jul 16, 2026Jul 16, 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
•11•31•10•1•Updated Jul 16, 2026Jul 16, 2026
mumble
Public
Finding the perfect modification for your mass shift
Python
•
Apache License 2.0
•1•6•0•0•Updated Jul 15, 2026Jul 15, 2026
peptide-gnn
Public
A graph-based deep learning model for predicting and explaining peptide LC-RT data.
Python
•
MIT License
•0•1•0•0•Updated Jul 14, 2026Jul 14, 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•5•0•Updated Jul 13, 2026Jul 13, 2026
compomics.com
Public
HTML
•0•0•1•0•Updated Jul 10, 2026Jul 10, 2026
mzdata-converter
Public
Bruker and Thermo raw file to mzML converter built with mzdata.
Rust
•
Apache License 2.0
•1•1•1•3•Updated Jul 9, 2026Jul 9, 2026
target_peptides_lookup
Public
TypeScript
•1•0•0•0•Updated Jul 9, 2026Jul 9, 2026
ThermoRawFileParser
Public
Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono
C#
•
Apache License 2.0
•60•250•15•1•Updated Jul 8, 2026Jul 8, 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•3•0•0•Updated Jul 7, 2026Jul 7, 2026
vizly
Public
Visualizations library for proteomics focusing on protein sequences, PTMs, peptides and peptide coverage
Vue
•
Apache License 2.0
•0•0•0•0•Updated Jun 22, 2026Jun 22, 2026
Peptonizer2000
Public
Confidence for taxonomic analysis in metaproteomics. Get ready to peptonize!
Python
•
Apache License 2.0
•1•3•3•1•Updated Jun 5, 2026Jun 5, 2026
tabloidProteome
Public
HTML
•
Apache License 2.0
•0•1•0•3•Updated Jun 5, 2026Jun 5, 2026
compomics-utilities
Public
Open source Java library for computational proteomics
bioinformatics proteomics computational-proteomics
bioinformatics proteomics computational-proteomics
Java
•18•37•8•2•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
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
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
D012554A_2025
Public
Jupyter Notebook
•
Apache License 2.0
•4•2•0•0•Updated Mar 19, 2026Mar 19, 2026

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Computational Omics and Systems Biology Group

All

All

114 repositories

DeepLC

eluflow

MuMDIA

peptide-shaker

ms2rescore

bioconda-recipes

SCI

ms2rescore-rs

CALLC3

ristretto

molcraft

IM2Deep

psm_utils

mumble

peptide-gnn

ms2pip

compomics.com

mzdata-converter

target_peptides_lookup

ThermoRawFileParser

iDeepLC

vizly

Peptonizer2000

tabloidProteome

compomics-utilities

omssa-parser

MoDPAv1.0

pdb-topology-viewer

protean-viz

D012554A_2025

All

All

Repositories list

114 repositories