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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 Loading

  1. comut comut Public

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

    Python 90 28

  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 16 5

  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 12 3

Repositories

Showing 10 of 61 repositories
  • pancan_germline_wgs Public

    Germline WGS variant calling across cancer types

    vanallenlab/pancan_germline_wgs’s past year of commit activity
    R 0 GPL-2.0 0 0 1 Updated Dec 13, 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 16 GPL-2.0 5 0 1 Updated Dec 11, 2024
  • germline-somatic-convergence Public

    Pilot exploration of overlap between germline and somatic alterations in common adult solid tumors

    vanallenlab/germline-somatic-convergence’s past year of commit activity
    R 0 GPL-2.0 0 0 0 Updated Dec 6, 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 Dec 6, 2024
  • beanie-analysis Public

    Code for reproducing results presented in the BEANIE paper

    vanallenlab/beanie-analysis’s past year of commit activity
    Jupyter Notebook 0 GPL-2.0 0 0 0 Updated Nov 15, 2024
  • miniconda Public

    Dockerfiles for Miniconda

    vanallenlab/miniconda’s past year of commit activity
    Dockerfile 3 GPL-2.0 0 0 0 Updated Nov 5, 2024
  • ped_germline_SV Public

    Analysis of germline SVs in pediatric cancers

    vanallenlab/ped_germline_SV’s past year of commit activity
    Jupyter Notebook 2 GPL-2.0 0 0 0 Updated Oct 31, 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 90 MIT 28 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
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