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@bhklab

BHKLAB

The Haibe-Kains Laboratory @ Princess Margaret Cancer Centre
README.md

Mission

Our overarching goal consists of developing cutting-edge computational tools and predictive models to identify new cancer vulnerabilities and improve the way precision oncology is delivered to patients.

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  1. PharmacoGx PharmacoGx Public

    R package to analyze large-scale pharmacogenomic datasets.

    R 71 26

  2. med-imagetools med-imagetools Public

    Transparent and reproducible medical image processing pipelines in Python.

    Python 56 10

  3. AnnotationGx AnnotationGx Public

    An R package to query various bio/chem-informatics databases APIs to construct annotation files.

    R 2 1

  4. readii readii Public

    Radiomic Extraction and Analysis for DICOM Images (READII)

    Jupyter Notebook 5

  5. orcestra-downloader orcestra-downloader Public

    Seamless CLI access to orcestra datasets

    Python 1

  6. handbook handbook Public

    Lab Handbook For BHKLab

    4

Repositories

Showing 10 of 239 repositories
  • orcestra-new-api Public
    bhklab/orcestra-new-api’s past year of commit activity
    Python 0 1 11 0 Updated Feb 9, 2026
  • PharmacoGx Public

    R package to analyze large-scale pharmacogenomic datasets.

    bhklab/PharmacoGx’s past year of commit activity
    R 71 GPL-3.0 26 74 3 Updated Feb 9, 2026
  • bhklab-nninteractive Public

    bhklab-nnInteractive is a project which tests the nnInteractive medical image segmentation model using RECIST and RERECIST input prompts and evaluates its performance.

    bhklab/bhklab-nninteractive’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Feb 6, 2026
  • spatial-analysis-framework-hnscc Public

    A Spatial Analysis Framework for Head and Neck Squamous Cell Carcinoma

    bhklab/spatial-analysis-framework-hnscc’s past year of commit activity
    R 0 0 13 0 Updated Feb 6, 2026
  • annotationdb-seeding Public

    Repository for creating and populating MySQL tables for AnnotationDB using SQLAlchemy

    bhklab/annotationdb-seeding’s past year of commit activity
    R 0 0 2 0 Updated Feb 6, 2026
  • annotationdb-api Public

    API for interfacing with AnnotationDB

    bhklab/annotationdb-api’s past year of commit activity
    Python 0 0 1 0 Updated Feb 4, 2026
  • dnf2 Public

    DNFv2 is the sequel to DNF using the tools from InteGrAO

    bhklab/dnf2’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Feb 2, 2026
  • MedSAM2-RECIST Public Forked from medfm-flare/MedSAM2-RECIST

    Docker-based MedSAM2 inference pipeline for MICCAI FLARE25 Task1-PancancerRECIST-to-3D

    bhklab/MedSAM2-RECIST’s past year of commit activity
    Python 0 Apache-2.0 1 0 0 Updated Jan 29, 2026
  • bhklab-BiomedParse Public Forked from microsoft/BiomedParse

    BiomedParse: A Foundation Model for Joint Segmentation, Detection, and Recognition of Biomedical Objects Across Nine Modalities

    bhklab/bhklab-BiomedParse’s past year of commit activity
    Python 0 Apache-2.0 95 0 0 Updated Jan 29, 2026
  • med-imagetools Public

    Transparent and reproducible medical image processing pipelines in Python.

    bhklab/med-imagetools’s past year of commit activity
    Python 56 MIT 10 29 (1 issue needs help) 4 Updated Jan 29, 2026
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