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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# 241 58

  2. DeepLC DeepLC Public

    DeepLC: Retention time prediction for peptides carrying any modification.

    Python 75 24

  3. ms2rescore ms2rescore Public

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

    Python 64 20

  4. compomics-utilities compomics-utilities Public

    Open source Java library for computational proteomics

    Java 34 17

  5. peptide-shaker peptide-shaker Public

    Interpretation of proteomics identification results

    Java 53 19

  6. searchgui searchgui Public

    Highly adaptable common interface for proteomics search and de novo engines

    Java 47 15

Repositories

Showing 10 of 106 repositories
  • pdb-topology-viewer Public Forked from PDBeurope/pdb-topology-viewer

    PDB Topology Viewer

    CompOmics/pdb-topology-viewer’s past year of commit activity
    TypeScript 0 Apache-2.0 5 0 0 Updated Apr 3, 2026
  • 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 2 Apache-2.0 2 0 0 Updated Apr 3, 2026
  • DeepLC Public

    DeepLC: Retention time prediction for peptides carrying any modification.

    CompOmics/DeepLC’s past year of commit activity
    Python 75 Apache-2.0 24 0 0 Updated Apr 2, 2026
  • 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 Apache-2.0 0 0 0 Updated Apr 2, 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 49 Apache-2.0 19 6 3 Updated Mar 31, 2026
  • ms2rescore Public

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

    CompOmics/ms2rescore’s past year of commit activity
    Python 64 Apache-2.0 20 10 9 Updated Mar 31, 2026
  • MuMDIA Public
    CompOmics/MuMDIA’s past year of commit activity
    Jupyter Notebook 2 Apache-2.0 0 3 (1 issue needs help) 1 Updated Mar 31, 2026
  • MoDPAv1.0 Public

    MoDPA repository for publication

    CompOmics/MoDPAv1.0’s past year of commit activity
    Jupyter Notebook 1 Apache-2.0 0 0 0 Updated Mar 25, 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 Mar 24, 2026
  • peptide-shaker Public

    Interpretation of proteomics identification results

    CompOmics/peptide-shaker’s past year of commit activity
    Java 53 19 46 (19 issues need help) 0 Updated Mar 21, 2026
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