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@vanallenlab

Van Allen Lab

Clinical Computational Oncology @ Dana-Farber Cancer Institute and the Broad Institute of MIT & Harvard
README.md

Hi there 👋

The Van Allen lab is a computational research group led by Eliezer Van Allen at Dana-Farber Cancer Institute, Harvard Medical School, and the Broad Institute whose mission is to drive precision cancer medicine through clinical computational oncology by:

  • Creating the engine to clinically interpret cancer genomes
  • Discovering response and resistance mechanisms to cancer therapies
  • Developing new ways to dissect cancer data
  • Exploring the inherited and environmental impact on cancer origins
  • Establishing the next generation of computational oncologists

You can learn more by visiting our lab website, reading our publications, and following us on Twitter.

Popular repositories

  1. comut comut Public

    CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots

    Python 87 25

  2. retained-intron-neoantigen-pipeline retained-intron-neoantigen-pipeline Public

    Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.

    Python 28 11

  3. schadendorf-pd1 schadendorf-pd1 Public

    code and data for Liu, Schilling, et al Nat Med 2019

    Jupyter Notebook 18 6

  4. moalmanac moalmanac Public

    Molecular Oncology Almanac, a clinical interpretation algorithm paired with a novel underlying knowledge base for precision cancer medicine

    HTML 15 4

  5. neoantigen_calling_pipeline neoantigen_calling_pipeline Public

    Pipeline to call somatic cancer neoantigens from mutations in patient tumor DNA

    Python 12 9

  6. facets facets Public

    Implementation of FACETS for Terra

    WDL 11 3

Repositories

Showing 10 of 59 repositories
  • pancan_germline_wgs Public

    Germline WGS variant calling across cancer types

    vanallenlab/pancan_germline_wgs’s past year of commit activity
    WDL 0 GPL-2.0 0 0 1 Updated Aug 20, 2024
  • ped_germline_SV Public

    Analysis of germline SVs in pediatric cancers

    vanallenlab/ped_germline_SV’s past year of commit activity
    R 2 GPL-2.0 0 0 0 Updated Aug 17, 2024
  • comut Public

    CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots

    vanallenlab/comut’s past year of commit activity
    Python 87 MIT 25 10 4 Updated Aug 1, 2024
  • schadendorf-pd1 Public

    code and data for Liu, Schilling, et al Nat Med 2019

    vanallenlab/schadendorf-pd1’s past year of commit activity
    Jupyter Notebook 18 GPL-2.0 6 1 0 Updated Aug 1, 2024
  • SigProfilerAssignment-wrapper Public

    Implementation repository for SigProfilerAssignment

    vanallenlab/SigProfilerAssignment-wrapper’s past year of commit activity
    Python 0 GPL-2.0 0 0 0 Updated Jul 12, 2024
  • moalmanac Public

    Molecular Oncology Almanac, a clinical interpretation algorithm paired with a novel underlying knowledge base for precision cancer medicine

    vanallenlab/moalmanac’s past year of commit activity
    HTML 15 GPL-2.0 4 0 1 Updated Jul 12, 2024
  • moalmanac-db Public

    Underlying content for the Molecular Oncology Almanac's database

    vanallenlab/moalmanac-db’s past year of commit activity
    5 GPL-2.0 1 0 0 Updated Jul 11, 2024
  • terra-helper Public

    Terra storage helper

    vanallenlab/terra-helper’s past year of commit activity
    Python 0 GPL-2.0 0 4 2 Updated May 21, 2024
  • moalmanac-browser Public

    Web portal interface for browsing the Molecular Oncology Almanac

    vanallenlab/moalmanac-browser’s past year of commit activity
    Python 1 GPL-2.0 1 0 2 Updated Apr 11, 2024
  • moalmanac-paper Public archive

    Analyses related to Reardon et al. 2021, Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology

    vanallenlab/moalmanac-paper’s past year of commit activity
    HTML 5 GPL-2.0 4 0 1 Updated Mar 13, 2024
View all repositories

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