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    41 repositories

    • casanovo

      Public
      De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
      Python
      •
      Apache License 2.0
      •48•149•22•4•Updated Jul 21, 2025Jul 21, 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-modelsmulti-omicschromatin-structurefoundation-models
      Python
      •
      Apache License 2.0
      •3•17•0•0•Updated Jul 17, 2025Jul 17, 2025

    • FDRBench

      Public
      Estimation of false discovery proportion for mass spectrometry proteomics data using entrapment
      Java
      •
      Apache License 2.0
      •2•17•5•0•Updated Jul 16, 2025Jul 16, 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

    • twinc

      Public
      TwinC: Twin CNN model for 3D genome folding
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Jul 8, 2025Jul 8, 2025

    • twinc_paper

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•1•0•0•Updated Jul 7, 2025Jul 7, 2025

    • Carafe

      Public
      High quality in silico spectral library generation for data-independent acquisition proteomics
      deep-learningproteomicsmass-spectrometrydata-independent-acquisitionspectral-library
      Java
      •
      Apache License 2.0
      •2•15•4•0•Updated Jul 3, 2025Jul 3, 2025

    • Sceptic

      Public
      Pseudotime analysis for time-series single-cell sequencing and imaging data
      time-seriessingle-cell-rna-seqsingle-cell-imagingpseudotime
      Jupyter Notebook
      •
      MIT License
      •1•8•0•0•Updated Jun 24, 2025Jun 24, 2025

    • hic-helper

      Public
      Python
      •0•5•0•0•Updated Jun 12, 2025Jun 12, 2025

    • lupine

      Public
      Mass spectrometry proteomics imputation with a multilayer perceptron
      machine-learningimputationproteomicsmass-spectrometry
      Python
      •
      MIT License
      •0•2•0•0•Updated Jun 10, 2025Jun 10, 2025

    • CellCycleNet

      Public
      Predicting cell cycle stage from 3D single-cell nuclear-stained images
      deep-learningsingle-celldapimicroscopy-imagescellcycle
      Python
      •
      MIT License
      •0•8•0•0•Updated Jun 2, 2025Jun 2, 2025

    • crema

      Public
      Confidence Estimation for Mass Spectrometry Proteomics
      Python
      •
      Other
      •2•13•2•0•Updated May 28, 2025May 28, 2025

    • nettle

      Public
      Nettle is an RT imputation method for MS proteomics
      imputationproteomicsmass-spectrometrymissing-valuesdata-independent-acquisition
      Python
      •
      MIT License
      •0•3•0•0•Updated May 16, 2025May 16, 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•1•0•Updated Apr 27, 2025Apr 27, 2025

    • FDRBench_manuscript

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •1•0•0•0•Updated Mar 24, 2025Mar 24, 2025

    • cascadia

      Public
      Transformer deep learning model for de novo sequencing of data-independent acquisition mass spectrometry data
      Python
      •
      Apache License 2.0
      •6•20•3•0•Updated Feb 14, 2025Feb 14, 2025

    • Icebear

      Public
      Python
      •
      Apache License 2.0
      •0•3•0•0•Updated Dec 4, 2024Dec 4, 2024

    • multi-species-benchmark

      Public
      Python
      •0•1•0•0•Updated Nov 8, 2024Nov 8, 2024

    • Sphinx

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Oct 17, 2024Oct 17, 2024

    • Sunbear

      Public
      single cell multimodal/multicondition temporal model
      Python
      •0•1•0•0•Updated Aug 27, 2024Aug 27, 2024

    • Polarbear

      Public
      Polarbear translates between different single-cell data modalities
      Python
      •
      Apache License 2.0
      •3•7•5•0•Updated Mar 20, 2024Mar 20, 2024

    • ACCOST

      Public
      Python
      •1•0•2•1•Updated Feb 22, 2024Feb 22, 2024

    • 2023-prot-impute-benchmark

      Public
      The GitHub repository accompanying our 2023 quantitative proteomics imputation methods benchmarking study
      Jupyter Notebook
      •
      MIT License
      •0•8•0•0•Updated Jul 26, 2023Jul 26, 2023

    • casanovo_asms2023

      Public
      ASMS 2023 De Novo Peptide Sequencing with Casanovo Workshop Materials
      Jupyter Notebook
      •
      Apache License 2.0
      •0•2•0•0•Updated Jun 5, 2023Jun 5, 2023

    • lda_matrix_prior

      Public
      Python
      •0•1•0•0•Updated Mar 8, 2023Mar 8, 2023

    • nih-latex

      Public
      Template for producing NIH grant proposals using latex
      TeX
      •
      MIT License
      •3•2•0•0•Updated Feb 7, 2023Feb 7, 2023

    • ALSO

      Public
      Shell
      •0•1•0•0•Updated Jan 25, 2023Jan 25, 2023

    • subset-neighbor-search

      Public
      Subset-neighbor-search is a method for FDR control from tandem mass spectrometry data, applicable when only a subset of peptides or proteins are of interest
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated Dec 23, 2022Dec 23, 2022

    • Pepper

      Public
      Peptide coefficient predictor
      Jupyter Notebook
      •
      Apache License 2.0
      •2•10•4•0•Updated Oct 19, 2022Oct 19, 2022