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@CompOmics

Computational Omics and Systems Biology Group

The CompOmics group, headed by Prof. Dr. Lennart Martens, specializes in the management, analysis and integration of high-throughput Omics data.

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  1. ThermoRawFileParser ThermoRawFileParser Public

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

    C# 230 54

  2. DeepLC DeepLC Public

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

    Python 70 24

  3. ms2rescore ms2rescore Public

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

    Python 61 20

  4. compomics-utilities compomics-utilities Public

    Open source Java library for computational proteomics

    Java 34 16

  5. peptide-shaker peptide-shaker Public

    Interpretation of proteomics identification results

    Java 52 18

  6. searchgui searchgui Public

    Highly adaptable common interface for proteomics search and de novo engines

    Java 46 15

Repositories

Showing 10 of 101 repositories
  • molcraft Public

    Deep Learning on Molecules.

    CompOmics/molcraft’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Nov 20, 2025
  • oui-discovery Public

    Collaboration between CompOmics & OpenProt group

    CompOmics/oui-discovery’s past year of commit activity
    Jupyter Notebook 0 Apache-2.0 0 0 0 Updated Nov 20, 2025
  • lsabd-machine-learning-tutorials Public

    Tutorials machine learning for the Large Scale Analysis of Biomedical Data course

    CompOmics/lsabd-machine-learning-tutorials’s past year of commit activity
    Jupyter Notebook 0 CC-BY-4.0 0 0 0 Updated Nov 4, 2025
  • ms2rescore-rs Public

    Rust functionality for the MS²Rescore package

    CompOmics/ms2rescore-rs’s past year of commit activity
    Rust 2 Apache-2.0 4 0 1 Updated Nov 4, 2025
  • protean-viz Public

    Tool to visualize user input such as modifications and peptides, including custom input files and search engine input files

    CompOmics/protean-viz’s past year of commit activity
    JavaScript 0 0 0 0 Updated Nov 4, 2025
  • Peptonizer2000 Public

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

    CompOmics/Peptonizer2000’s past year of commit activity
    Python 1 Apache-2.0 0 3 0 Updated Nov 3, 2025
  • tabloidProteome Public
    CompOmics/tabloidProteome’s past year of commit activity
    HTML 1 Apache-2.0 0 0 3 Updated Nov 1, 2025
  • iDeepLC Public

    iDeepLC: A deep Learning-based retention time predictor for unseen modified peptides with a novel encoding system

    CompOmics/iDeepLC’s past year of commit activity
    Python 1 Apache-2.0 1 0 0 Updated Oct 29, 2025
  • psm_utils Public

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

    CompOmics/psm_utils’s past year of commit activity
    Python 29 Apache-2.0 10 8 (2 issues need help) 1 Updated Oct 28, 2025
  • ThermoRawFileParser Public

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

    CompOmics/ThermoRawFileParser’s past year of commit activity
    C# 230 Apache-2.0 54 10 0 Updated Oct 27, 2025
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