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@Noble-Lab

Noble Lab Department of Genome Sciences UW

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  1. casanovo casanovo Public

    De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model

    Python 172 54

  2. cascadia cascadia Public

    Transformer deep learning model for de novo sequencing of data-independent acquisition mass spectrometry data

    Python 26 12

  3. HiCFoundation HiCFoundation Public

    HiCFoundation is a generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species.

    Python 25 4

  4. FDRBench FDRBench Public

    Estimation of false discovery proportion for mass spectrometry proteomics data using entrapment

    Java 22 3

  5. Carafe Carafe Public

    High quality in silico spectral library generation for data-independent acquisition proteomics

    Java 16 3

  6. crema crema Public

    Confidence Estimation for Mass Spectrometry Proteomics

    Python 13 2

Repositories

Showing 10 of 46 repositories
  • hic-helper Public
    Noble-Lab/hic-helper’s past year of commit activity
    Python 5 0 0 0 Updated Dec 27, 2025
  • hic_scaffolder_benchmarks Public

    A benchmarking study exploring the accuracy of popular Hi-C scaffolders.

    Noble-Lab/hic_scaffolder_benchmarks’s past year of commit activity
    Shell 2 MIT 0 0 0 Updated Dec 24, 2025
  • casanovo Public

    De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model

    Noble-Lab/casanovo’s past year of commit activity
    Python 172 Apache-2.0 54 26 (3 issues need help) 8 Updated Dec 23, 2025
  • Puget Public

    Deep learning model for predicting gene expression across cell types using sequence and 3D chromatin organization data

    Noble-Lab/Puget’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated Dec 10, 2025
  • 2025_gmurtaza_hicviz Public

    A simple toolkit to visually compare two Hi-C contact matrices

    Noble-Lab/2025_gmurtaza_hicviz’s past year of commit activity
    Python 0 0 0 0 Updated Dec 1, 2025
  • 2025_gmurtaza_loop-qc Public

    All the code to gather QC metrics for chromatin loop data

    Noble-Lab/2025_gmurtaza_loop-qc’s past year of commit activity
    Python 0 0 0 0 Updated Nov 26, 2025
  • Sceptic Public

    Pseudotime analysis for time-series single-cell sequencing and imaging data

    Noble-Lab/Sceptic’s past year of commit activity
    Jupyter Notebook 12 MIT 1 0 0 Updated Nov 13, 2025
  • Carafe Public

    High quality in silico spectral library generation for data-independent acquisition proteomics

    Noble-Lab/Carafe’s past year of commit activity
    Java 16 Apache-2.0 3 4 0 Updated Nov 6, 2025
  • cascadia Public

    Transformer deep learning model for de novo sequencing of data-independent acquisition mass spectrometry data

    Noble-Lab/cascadia’s past year of commit activity
    Python 26 Apache-2.0 12 7 (1 issue needs help) 2 Updated Oct 31, 2025
  • nettle Public

    Nettle is an RT imputation method for MS proteomics

    Noble-Lab/nettle’s past year of commit activity
    Python 3 MIT 0 0 0 Updated Oct 14, 2025

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