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    52 repositories

    • casanovo

      Public
      De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
      Python
      •
      Apache License 2.0
      •75•189•19•5•Updated Jun 23, 2026Jun 23, 2026

    • crema

      Public
      Confidence Estimation for Mass Spectrometry Proteomics
      Python
      •
      Other
      •2•14•2•5•Updated Jun 21, 2026Jun 21, 2026

    • Carafe

      Public
      High quality in silico spectral library generation for data-independent acquisition proteomics
      deep-learningproteomicsmass-spectrometry
      deep-learningproteomicsmass-spectrometrydata-independent-acquisitionspectral-library
      Java
      •
      Apache License 2.0
      •4•22•3•0•Updated Jun 19, 2026Jun 19, 2026

    • CasanovoGUI

      Public
      CasanovoGUI: a cross-platform desktop application for Casanovo
      deep-learningproteomicsmass-spectrometry
      deep-learningproteomicsmass-spectrometrypeptide-denovo-sequencing
      Java
      •0•0•0•1•Updated Jun 18, 2026Jun 18, 2026

    • Puget-preprint

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 14, 2026Jun 14, 2026

    • FDRBench

      Public
      Estimation of false discovery proportion for mass spectrometry proteomics data using entrapment
      Java
      •
      Apache License 2.0
      •3•32•4•0•Updated Jun 9, 2026Jun 9, 2026

    • bromo-manuscript

      Public
      All scripts and code to reproduce figures from "Prioritizing peptides for targeted mass spectrometry experiments using deep learning"
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated May 26, 2026May 26, 2026

    • bromo

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated May 26, 2026May 26, 2026

    • glissade

      Public
      FDR control for mass spectrometry analysis using de novo and database search results
      Python
      •1•2•1•0•Updated May 8, 2026May 8, 2026

    • casanovoutils

      Public
      Python
      •0•1•4•1•Updated Apr 27, 2026Apr 27, 2026

    • MIMIR

      Public
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Apr 24, 2026Apr 24, 2026

    • casanovo-foundation

      Public
      A foundation model for mass spectrometry proteomics
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 7, 2026Apr 7, 2026

    • multi-species-benchmark

      Public
      Python
      •0•1•0•0•Updated Mar 13, 2026Mar 13, 2026

    • Sceptic

      Public
      Pseudotime analysis for time-series single-cell sequencing and imaging data
      time-seriessingle-cell-rna-seqsingle-cell-imaging
      time-seriessingle-cell-rna-seqsingle-cell-imagingpseudotime
      Jupyter Notebook
      •
      MIT License
      •2•13•0•0•Updated Mar 13, 2026Mar 13, 2026

    • cascadia

      Public
      Transformer deep learning model for de novo sequencing of data-independent acquisition mass spectrometry data
      Python
      •
      Apache License 2.0
      •14•33•5•0•Updated Mar 3, 2026Mar 3, 2026

    • twinc_paper

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•1•0•0•Updated Feb 17, 2026Feb 17, 2026

    • twinc

      Public
      TwinC: Twin CNN model for 3D genome folding
      Python
      •
      Apache License 2.0
      •0•3•0•0•Updated Feb 17, 2026Feb 17, 2026

    • hic-helper

      Public
      Python
      •0•4•0•0•Updated Dec 27, 2025Dec 27, 2025

    • hic_scaffolder_benchmarks

      Public
      A benchmarking study exploring the accuracy of popular Hi-C scaffolders.
      Shell
      •
      MIT License
      •0•2•0•0•Updated Dec 24, 2025Dec 24, 2025

    • 2025_gmurtaza_hicviz

      Public
      A simple toolkit to visually compare two Hi-C contact matrices
      Python
      •0•0•0•0•Updated Dec 1, 2025Dec 1, 2025

    • 2025_gmurtaza_loop-qc

      Public
      All the code to gather QC metrics for chromatin loop data
      Python
      •0•0•0•0•Updated Nov 26, 2025Nov 26, 2025

    • nettle

      Public
      Nettle is an RT imputation method for MS proteomics
      imputationproteomicsmass-spectrometry
      imputationproteomicsmass-spectrometrymissing-valuesdata-independent-acquisition
      Python
      •
      MIT License
      •0•3•0•0•Updated Oct 14, 2025Oct 14, 2025

    • 2025_MOHD_hackathon

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Sep 19, 2025Sep 19, 2025

    • HiCFoundation

      Public
      HiCFoundation is a generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species.
      deep-learninghi-clarge-models
      deep-learninghi-clarge-modelsmulti-omicschromatin-structurefoundation-models
      Python
      •
      Apache License 2.0
      •4•31•1•0•Updated Aug 23, 2025Aug 23, 2025

    • Sunbear

      Public
      single cell multimodal/multicondition temporal model
      Python
      •0•3•0•0•Updated Jul 25, 2025Jul 25, 2025

    • 2024_proteomics_impute

      Public
      Code used to generate figures in our 2024 manuscript on mass spectrometry proteomics imputation
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

    • lupine

      Public
      Mass spectrometry proteomics imputation with a multilayer perceptron
      machine-learningimputationproteomics
      machine-learningimputationproteomicsmass-spectrometry
      Python
      •
      MIT License
      •1•4•0•0•Updated Jun 10, 2025Jun 10, 2025

    • CellCycleNet

      Public
      Predicting cell cycle stage from 3D single-cell nuclear-stained images
      deep-learningsingle-celldapi
      deep-learningsingle-celldapimicroscopy-imagescellcycle
      Python
      •
      MIT License
      •0•10•0•0•Updated Jun 2, 2025Jun 2, 2025

    • HiCFoundation_paper

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•3•0•0•Updated May 13, 2025May 13, 2025

    • trans-C

      Public
      Identifying sets of loci that interact strongly in trans
      Python
      •
      MIT License
      •0•4•2•0•Updated Apr 27, 2025Apr 27, 2025
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