Repositories list

• MuMDIA

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •0•1•1•0•Updated Feb 6, 2025Feb 6, 2025

• DeepLC

  Public
  DeepLC: Retention time prediction for (modified) peptides using Deep Learning.

  deep-learningproteomicspeptides+ 2retention-timepeptide-modification

  Python

  •

  Apache License 2.0

  •19•58•0•0•Updated Feb 3, 2025Feb 3, 2025

• molexpress

  Public
  Graph Neural Networks with Keras 3

  Python

  •

  MIT License

  •1•0•0•1•Updated Jan 31, 2025Jan 31, 2025

• IM2Deep

  Public
  Collisional cross-section prediction for modified peptides

  proteomicsmass-spectrometrypeptides+ 3ion-mobilitycollisional-cross-sectiontimstof

  Python

  •

  Apache License 2.0

  •0•7•0•1•Updated Jan 31, 2025Jan 31, 2025

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.4k•0•0•0•Updated Jan 30, 2025Jan 30, 2025

• ms2rescore

  Public
  Modular and user-friendly platform for AI-assisted rescoring of peptide identifications

  proteomicspercolatorpeptide-identification+ 2ms2pipdeeplc

  Python

  •

  Apache License 2.0

  •16•53•14•2•Updated Jan 24, 2025Jan 24, 2025

• Peptonizer2000

  Public
  Confidence for taxonomic analysis in metaproteomics. Get ready to peptonize!

  Python

  •

  Apache License 2.0

  •0•1•3•0•Updated Jan 22, 2025Jan 22, 2025

• mumble

  Public
  Finding the perfect modification for your mass shift

  Python

  •

  Apache License 2.0

  •1•4•1•2•Updated Jan 21, 2025Jan 21, 2025

• ms2pip

  Public
  MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.

  machine-learningproteomicsmass-spectrometry+ 3peptide-identificationspectrum-predictionpeptide-spectrum

  HTML

  •

  Apache License 2.0

  •18•40•11•1•Updated Jan 21, 2025Jan 21, 2025

• compomics.github.io

  Public
  Compomics github website.

  SCSS

  •

  MIT License

  •1•0•0•0•Updated Jan 21, 2025Jan 21, 2025

• psm_utils

  Public
  Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python

  pythonparsingproteomics+ 3mass-spectrometrypeptide-identificationpeptide-spectrum-matches

  Python

  •

  Apache License 2.0

  •8•26•7•1•Updated Jan 20, 2025Jan 20, 2025

• ms2rescore-rs

  Public
  Rust functionality for the MS²Rescore package

  Rust

  •

  Apache License 2.0

  •0•2•0•0•Updated Jan 15, 2025Jan 15, 2025

• ThermoRawFileParser

  Public
  Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono

  C#

  •

  Apache License 2.0

  •49•198•16•1•Updated Jan 2, 2025Jan 2, 2025

• compomics-utilities

  Public
  Open source Java library for computational proteomics

  proteomicscomputational-proteomicsbioinformatics

  Java

  •17•32•4•0•Updated Dec 20, 2024Dec 20, 2024

• peptide-shaker

  Public
  Interpretation of proteomics identification results

  proteomicsprotein-identificationjava+ 1bioinformatics

  Java

  •18•48•37•0•Updated Dec 20, 2024Dec 20, 2024

• ML-course-VIB-2024

  Public
  Jupyter Notebook

  •51•8•0•0•Updated Nov 26, 2024Nov 26, 2024

• search-all-assess-subset-paper

  Public archive
  HTML

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• Tissue_prediction_manuscript

  Public archive
  Jupyter Notebook

  •1•1•0•0•Updated Nov 18, 2024Nov 18, 2024

• electron-vue-python-boilerplate

  Public
  Boilerplate to create desktop applications with electron, Vue3 and FastAPI

  Vue

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• lesSDRF

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •8•6•3•2•Updated Sep 27, 2024Sep 27, 2024

• searchgui

  Public
  Highly adaptable common interface for proteomics search and de novo engines

  proteomicsprotein-identificationjava+ 1bioinformatics

  Java

  •15•43•16•0•Updated Sep 19, 2024Sep 19, 2024

• reporter

  Public
  Protein quantification based on reporter ions

  bioinformaticsproteomicsprotein-quantification+ 1reporter-ions

  Java

  •2•4•5•0•Updated Sep 10, 2024Sep 10, 2024

• ThermoRawFileParserGUI

  Public
  Graphical user interface for the ThermoRawFileParser

  conversionproteomicsraw+ 1java

  Java

  •

  Apache License 2.0

  •0•20•1•0•Updated Jul 5, 2024Jul 5, 2024

• tabloidProteome

  Public
  HTML

  •

  Apache License 2.0

  •0•1•0•3•Updated Mar 21, 2024Mar 21, 2024

• denovogui

  Public
  Graphical user interface for de novo sequencing of tandem mass spectra

  proteomicsdenovographical-user-interface+ 1de-novo-sequencing

  Java

  •7•14•4•0•Updated Mar 11, 2024Mar 11, 2024

• workshop-BioscienceSnapshot

  Public
  Dockerfile

  •

  Creative Commons Attribution Share Alike 4.0 International

  •1•0•0•0•Updated Oct 9, 2023Oct 9, 2023

• COSS

  Public
  COSS: CompOmics Spectral Searching

  Java

  •3•8•5•4•Updated Apr 18, 2023Apr 18, 2023

• moff-gui

  Public
  A graphical user interface for the Modest Feature Finding algorithm (moFF)

  Java

  •2•2•0•1•Updated Mar 11, 2023Mar 11, 2023

• CALLC

  Public
  Python

  •

  Apache License 2.0

  •1•6•1•0•Updated Mar 6, 2023Mar 6, 2023

• jsparklines

  Public
  Sparklines for java tables

  visualizationsparkline

  Java

  •3•8•2•0•Updated Mar 1, 2023Mar 1, 2023