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@BaderLab

Bader Lab, University of Toronto

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  1. saber saber Public

    Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work in progress. Many things are broken, and the codebase is not…

    Python 102 17

  2. CellAnnotationTutorial CellAnnotationTutorial Public

    Accompanying code for the tutorial: Annotating single cell transcriptomic maps using automated and manual methods

    HTML 99 24

  3. scClustViz scClustViz Public

    Explore and share your scRNAseq clustering results

    R 53 10

  4. Cytoscape_workflows Cytoscape_workflows Public

    collection of notebooks with different cytoscape workflows

    HTML 51 38

  5. EnrichmentMapApp EnrichmentMapApp Public

    The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.

    Java 37 12

  6. Transfer-Learning-BNER-Bioinformatics-2018 Transfer-Learning-BNER-Bioinformatics-2018 Public

    This repository contains supplementary data, and links to the model and corpora used for the paper: Transfer learning for biomedical named entity recognition with neural networks.

    Python 37 6

Repositories

Showing 10 of 100 repositories
  • MCODE Public

    Cytoscape app that clusters a given network based on topology to find densely connected regions

    BaderLab/MCODE's past year of commit activity
    Java 11 6 3 1 Updated Sep 8, 2026
  • GenAnT Public

    A tutorial on how to annotate and interpret novel mammalian reference genomes

    BaderLab/GenAnT's past year of commit activity
    HTML 29 MIT 8 1 0 Updated Aug 22, 2026
  • DeepvEM Public
    1 0 0 0 Updated Aug 21, 2026
  • ecuda Public

    STL-style abstractions for CUDA.

    BaderLab/ecuda's past year of commit activity
    C++ 33 Apache-2.0 7 0 1 Updated Aug 18, 2026
  • cy3d-impl Public

    3D Graph Renderer for Cytoscape using OpenGL

    BaderLab/cy3d-impl's past year of commit activity
    Java 10 1 6 0 Updated Aug 2, 2026
  • MuST-EM Public
    BaderLab/MuST-EM's past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Aug 2, 2026
  • malatin Public
    BaderLab/malatin's past year of commit activity
    R 19 5 0 0 Updated Jul 28, 2026
  • BaderLab/Multiscale_human_liver_vEM's past year of commit activity
    Jupyter Notebook 1 MIT 0 0 0 Updated Apr 15, 2026
  • FLASHMM Public

    Fast and Scalable Single Cell Differential Expression Analysis using Mixed-effects Models

    BaderLab/FLASHMM's past year of commit activity
    R 12 2 15 1 Updated Apr 8, 2026
  • BaderLab/Lineage_Theory's past year of commit activity
    Wolfram Language 0 0 0 0 Updated Feb 27, 2026

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