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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# 223 53

  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 60 19

  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 50 18

  6. searchgui searchgui Public

    Highly adaptable common interface for proteomics search and de novo engines

    Java 45 15

Repositories

Showing 10 of 99 repositories
  • 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 Sep 12, 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 Sep 12, 2025
  • tabloidProteome Public
    CompOmics/tabloidProteome’s past year of commit activity
    HTML 1 Apache-2.0 0 0 3 Updated Sep 12, 2025
  • MuMDIA Public
    CompOmics/MuMDIA’s past year of commit activity
    Jupyter Notebook 2 Apache-2.0 0 5 (1 issue needs help) 3 Updated Sep 11, 2025
  • ecoli-peptideatlas-manuscript Public

    Code used to produce figures in the E. coli PeptideAtlas Paper

    CompOmics/ecoli-peptideatlas-manuscript’s past year of commit activity
    Jupyter Notebook 1 Apache-2.0 0 0 0 Updated Sep 11, 2025
  • molcraft Public

    Deep Learning on Molecules.

    CompOmics/molcraft’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 8, 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# 223 Apache-2.0 53 17 1 Updated Sep 5, 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 0 Apache-2.0 1 0 0 Updated Sep 4, 2025
  • DeepLC Public

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

    CompOmics/DeepLC’s past year of commit activity
    Python 70 Apache-2.0 24 0 1 Updated Sep 1, 2025
  • reporter Public

    Protein quantification based on reporter ions

    CompOmics/reporter’s past year of commit activity
    Java 4 2 5 (3 issues need help) 0 Updated Aug 15, 2025
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