Skip to content
Change the repository type filter

All

    Repositories list

    • FDRBench

      Public
      Estimation of false discovery proportion for mass spectrometry proteomics data using entrapment
      Java
      Apache License 2.0
      11140Updated Jun 19, 2025Jun 19, 2025
    • casanovo

      Public
      De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
      Python
      Apache License 2.0
      48142249Updated Jun 18, 2025Jun 18, 2025
    • Python
      0500Updated Jun 12, 2025Jun 12, 2025
    • lupine

      Public
      Mass spectrometry proteomics imputation with a multilayer perceptron
      Python
      MIT License
      0200Updated Jun 10, 2025Jun 10, 2025
    • HiCFoundation is a generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species.
      Python
      Apache License 2.0
      31700Updated Jun 9, 2025Jun 9, 2025
    • twinc

      Public
      TwinC: Twin CNN model for 3D genome folding
      Python
      Apache License 2.0
      0200Updated Jun 4, 2025Jun 4, 2025
    • Predicting cell cycle stage from 3D single-cell nuclear-stained images
      Python
      MIT License
      0800Updated Jun 2, 2025Jun 2, 2025
    • crema

      Public
      Confidence Estimation for Mass Spectrometry Proteomics
      Python
      Other
      21220Updated May 28, 2025May 28, 2025
    • Carafe

      Public
      High quality in silico spectral library generation for data-independent acquisition proteomics
      Java
      Apache License 2.0
      21440Updated May 20, 2025May 20, 2025
    • nettle

      Public
      Nettle is an RT imputation method for MS proteomics
      Python
      MIT License
      0300Updated May 16, 2025May 16, 2025
    • Jupyter Notebook
      Apache License 2.0
      0300Updated May 13, 2025May 13, 2025
    • trans-C

      Public
      Identifying sets of loci that interact strongly in trans
      Python
      MIT License
      0410Updated Apr 27, 2025Apr 27, 2025
    • Sceptic

      Public
      Pseudotime analysis for time-series single-cell sequencing and imaging data
      Jupyter Notebook
      MIT License
      1700Updated Apr 22, 2025Apr 22, 2025
    • Jupyter Notebook
      Apache License 2.0
      0000Updated 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
      51230Updated Feb 14, 2025Feb 14, 2025
    • Icebear

      Public
      Python
      Apache License 2.0
      0300Updated Dec 4, 2024Dec 4, 2024
    • Python
      0100Updated Nov 8, 2024Nov 8, 2024
    • Sphinx

      Public
      Jupyter Notebook
      0100Updated Oct 17, 2024Oct 17, 2024
    • Code used to generate figures in our 2024 manuscript on mass spectrometry proteomics imputation
      Jupyter Notebook
      MIT License
      0000Updated Sep 12, 2024Sep 12, 2024
    • Sunbear

      Public
      single cell multimodal/multicondition temporal model
      Python
      0100Updated Aug 27, 2024Aug 27, 2024
    • Polarbear

      Public
      Polarbear translates between different single-cell data modalities
      Python
      Apache License 2.0
      3750Updated Mar 20, 2024Mar 20, 2024
    • ACCOST

      Public
      Python
      1021Updated Feb 22, 2024Feb 22, 2024
    • The GitHub repository accompanying our 2023 quantitative proteomics imputation methods benchmarking study
      Jupyter Notebook
      MIT License
      0800Updated Jul 26, 2023Jul 26, 2023
    • ASMS 2023 De Novo Peptide Sequencing with Casanovo Workshop Materials
      Jupyter Notebook
      Apache License 2.0
      0200Updated Jun 5, 2023Jun 5, 2023
    • Python
      0100Updated Mar 8, 2023Mar 8, 2023
    • nih-latex

      Public
      Template for producing NIH grant proposals using latex
      TeX
      MIT License
      3200Updated Feb 7, 2023Feb 7, 2023
    • ALSO

      Public
      Shell
      0100Updated Jan 25, 2023Jan 25, 2023
    • 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
      0200Updated Dec 23, 2022Dec 23, 2022
    • Pepper

      Public
      Peptide coefficient predictor
      Jupyter Notebook
      Apache License 2.0
      21040Updated Oct 19, 2022Oct 19, 2022
    • R
      0100Updated Sep 28, 2022Sep 28, 2022