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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 98 25

  3. scClustViz scClustViz Public

    Explore and share your scRNAseq clustering results

    R 50 9

  4. Cytoscape_workflows Cytoscape_workflows Public

    collection of notebooks with different cytoscape workflows

    HTML 50 38

  5. 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

  6. Biomedical-Corpora Biomedical-Corpora Public

    A collection of annotated biomedical corpora, which can be used for training supervised machine learning methods for various tasks in biomedical text-mining and information extraction.

    36 4

Repositories

Showing 10 of 96 repositories
  • BaderLab/phase_contrast_collective_organization_GSCs_incucyte_August2025’s past year of commit activity
    R 0 MIT 0 0 0 Updated Dec 25, 2025
  • GenAnT Public

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

    BaderLab/GenAnT’s past year of commit activity
    HTML 6 MIT 2 0 0 Updated Dec 24, 2025
  • FLASH-MM-analysis Public

    Analysis scripts for benchmarking FLASH-MM and applying it to case-control and cell-type-specific comparisons in scRNA-seq datasets.

    BaderLab/FLASH-MM-analysis’s past year of commit activity
    R 0 MIT 0 0 0 Updated Dec 8, 2025
  • FLASHMM Public

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

    BaderLab/FLASHMM’s past year of commit activity
    R 7 1 11 1 Updated Aug 27, 2025
  • APA-Net Public
    BaderLab/APA-Net’s past year of commit activity
    Jupyter Notebook 1 MIT 0 0 0 Updated Aug 14, 2025
  • RETINA Public
    BaderLab/RETINA’s past year of commit activity
    Jupyter Notebook 3 MIT 0 0 0 Updated Jun 16, 2025
  • ComputeOntario_Pathways_2025 Public Forked from BaderLab/CBW_Pathways_2024_asynchronous

    Compute Ontario Pathway and Network Analysis Bookdown for June 2025

    BaderLab/ComputeOntario_Pathways_2025’s past year of commit activity
    CSS 2 CC0-1.0 11 0 0 Updated Jun 4, 2025
  • BaderLab/MALAT1_threshold’s past year of commit activity
    R 15 MIT 4 0 0 Updated May 22, 2025
  • GSEA_vs_fGSEA Public Forked from risserlin/CBW_pathways_workshop_R_notebooks

    compare results from GSEA and fGSEA

    BaderLab/GSEA_vs_fGSEA’s past year of commit activity
    TeX 0 CC0-1.0 2 0 0 Updated Apr 30, 2025
  • sciRED Public
    BaderLab/sciRED’s past year of commit activity
    Jupyter Notebook 7 MIT 2 1 0 Updated Mar 20, 2025