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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 85 23

  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 16 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 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 11 3

Repositories

Showing 10 of 58 repositories
  • terra-helper Public

    Terra storage helper

    Python 0 GPL-2.0 0 4 2 Updated May 21, 2024
  • pancan_germline_wgs Public

    Germline WGS variant calling across cancer types

    WDL 0 GPL-2.0 0 0 1 Updated May 17, 2024
  • moalmanac Public

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

    HTML 15 GPL-2.0 5 0 0 Updated May 15, 2024
  • ped_germline_SV Public

    Analysis of germline SVs in pediatric cancers

    R 2 GPL-2.0 0 0 0 Updated May 1, 2024
  • moalmanac-db Public

    Underlying content for the Molecular Oncology Almanac's database

    5 GPL-2.0 1 0 0 Updated Apr 11, 2024
  • moalmanac-browser Public

    Web portal interface for browsing the Molecular Oncology Almanac

    Python 1 GPL-2.0 1 0 2 Updated Apr 11, 2024
  • SigProfilerAssignment-wrapper Public

    Implementation repository for SigProfilerAssignment

    Python 0 GPL-2.0 0 0 0 Updated Apr 5, 2024
  • comut Public

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

    Python 85 MIT 23 10 3 Updated Apr 3, 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

    HTML 5 GPL-2.0 4 0 1 Updated Mar 13, 2024
  • pnet Public

    Implementation of P-Net as a flexible deep learning tool to generate insights from genetic features.

    Jupyter Notebook 1 GPL-2.0 2 0 0 Updated Feb 12, 2024
View all repositories

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