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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# 233 55

  2. DeepLC DeepLC Public

    DeepLC: Retention time prediction for peptides carrying any modification.

    Python 72 24

  3. ms2rescore ms2rescore Public

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

    Python 62 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 53 18

  6. searchgui searchgui Public

    Highly adaptable common interface for proteomics search and de novo engines

    Java 46 15

Repositories

Showing 10 of 102 repositories
  • DeepLC Public

    DeepLC: Retention time prediction for peptides carrying any modification.

    CompOmics/DeepLC’s past year of commit activity
    Python 72 Apache-2.0 24 0 1 Updated Jan 13, 2026
  • IM2Deep Public

    Collisional cross-section prediction for modified and multiconformational peptides

    CompOmics/IM2Deep’s past year of commit activity
    Python 13 Apache-2.0 2 0 1 Updated Jan 13, 2026
  • MoDPAv1.0 Public

    MoDPA repository for publication

    CompOmics/MoDPAv1.0’s past year of commit activity
    Jupyter Notebook 0 Apache-2.0 0 0 0 Updated Jan 13, 2026
  • ms2rescore Public

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

    CompOmics/ms2rescore’s past year of commit activity
    Python 62 Apache-2.0 20 13 3 Updated Jan 12, 2026
  • ms2pip Public

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

    CompOmics/ms2pip’s past year of commit activity
    HTML 47 Apache-2.0 19 7 4 Updated Jan 9, 2026
  • 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 Jan 8, 2026
  • 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 2 Updated Jan 6, 2026
  • 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# 233 Apache-2.0 55 10 0 Updated Jan 6, 2026
  • molcraft Public

    Deep learning on molecules: Minimalistic and powerful implementations of molecular graphs and graph neural networks.

    CompOmics/molcraft’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Jan 6, 2026
  • 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 Dec 22, 2025
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