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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 91 27

  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 63 repositories
  • 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 1 2 Updated Feb 26, 2025
  • 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 Feb 25, 2025
  • moalmanac-db Public

    Underlying content for the Molecular Oncology Almanac's database

    vanallenlab/moalmanac-db’s past year of commit activity
    6 GPL-2.0 1 0 1 Updated Feb 18, 2025
  • moalmanac-matchmaking Public

    Template repository to perform profile-to-cell line matchmaking

    vanallenlab/moalmanac-matchmaking’s past year of commit activity
    Python 0 GPL-2.0 0 3 0 Updated Feb 10, 2025
  • 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 1 1 Updated Feb 7, 2025
  • clinicogenomics-FriendsDontLetFriends Public

    Directly inspired from Chenxin Li's "Friends Don't Let Friends Make Bad Graphs"

    vanallenlab/clinicogenomics-FriendsDontLetFriends’s past year of commit activity
    0 GPL-2.0 0 0 0 Updated Feb 4, 2025
  • 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 Jan 29, 2025
  • chek2_germline Public

    Analysis of germline genetic variants in CHEK2

    vanallenlab/chek2_germline’s past year of commit activity
    WDL 0 GPL-2.0 0 0 0 Updated Jan 29, 2025
  • beanie Public

    Tool for group biology estimation in single-cell RNAseq data

    vanallenlab/beanie’s past year of commit activity
    Python 5 GPL-2.0 1 0 0 Updated Jan 8, 2025
  • 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 Jan 8, 2025
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