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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 88 25

  3. Cytoscape_workflows Cytoscape_workflows Public

    collection of notebooks with different cytoscape workflows

    HTML 48 36

  4. scClustViz scClustViz Public

    Explore and share your scRNAseq clustering results

    R 46 9

  5. 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.

    37 4

  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 36 6

Repositories

Showing 10 of 87 repositories
  • CBW_Pathways_2024_asynchronous Public Forked from BaderLab/CBW_Pathways_2024

    CBW Asynchronous Pathway and Network Analysis Bookdown for November 2024

    BaderLab/CBW_Pathways_2024_asynchronous’s past year of commit activity
    Jupyter Notebook 0 CC0-1.0 6 0 0 Updated Nov 6, 2024
  • BaderLab/EnrichmentMap_monthlyGenesetBuild’s past year of commit activity
    Java 2 0 9 0 Updated Nov 5, 2024
  • RETINA Public
    BaderLab/RETINA’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Oct 31, 2024
  • EnrichmentMap_docs Public

    End-User Documentation for the EnrichmentMap Cytoscape App

    BaderLab/EnrichmentMap_docs’s past year of commit activity
    Python 3 1 2 0 Updated Oct 7, 2024
  • EnrichmentMapApp Public

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

    BaderLab/EnrichmentMapApp’s past year of commit activity
    Java 32 LGPL-2.1 12 30 9 Updated Oct 7, 2024
  • AutoAnnotateApp Public

    The AutoAnnotate Cytoscape App finds clusters of nodes and visually annotates them with semantic labels and groups.

    BaderLab/AutoAnnotateApp’s past year of commit activity
    Java 6 LGPL-2.1 1 20 3 Updated Oct 7, 2024
  • openPIP Public

    The open protein interaction platform repo

    BaderLab/openPIP’s past year of commit activity
    JavaScript 7 MIT 9 16 0 Updated Aug 6, 2024
  • BaderLab/MALAT1_threshold’s past year of commit activity
    R 9 MIT 1 0 0 Updated Jul 22, 2024
  • CBW_Pathways_2024 Public Forked from BaderLab/CBW_Pathways_2023

    CBW Pathway and Network Analysis Bookdown for June 2024

    BaderLab/CBW_Pathways_2024’s past year of commit activity
    Jupyter Notebook 0 CC0-1.0 6 1 0 Updated Jun 28, 2024
  • ecuda Public

    STL-like containers (array, vector, matrix, cube) useable in device code.

    BaderLab/ecuda’s past year of commit activity
    C++ 31 5 0 0 Updated Feb 23, 2024

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