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    72 repositories

    • pancan_germline_wgs

      Public
      Germline WGS variant calling across cancer types
      R
      •
      GNU General Public License v2.0
      •0•0•0•1•Updated Feb 3, 2026Feb 3, 2026

    • moalmanac

      Public
      Molecular Oncology Almanac, a clinical interpretation algorithm paired with a novel underlying knowledge base for precision cancer medicine
      pythonprecision-cancer-medicinemolecular-oncology-almanacclinical-interpretation-algorithm
      HTML
      •
      GNU General Public License v2.0
      •6•17•6•2•Updated Feb 2, 2026Feb 2, 2026

    • unexplained_familial_cancer

      Public
      This repository (currently work in progress) is used to store the code and findings exploring genomic causes of Unexplained Familial Cancer.
      WDL
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 1, 2026Feb 1, 2026

    • moalmanac-db

      Public
      Underlying content for the Molecular Oncology Almanac's database
      precision-cancer-medicinemolecular-oncology-almanac
      Python
      •
      GNU General Public License v2.0
      •4•6•20•0•Updated Feb 1, 2026Feb 1, 2026

    • moalmanac-api

      Public
      API for moalmanac db and web browser 2.0
      molecular-oncology-almanac
      Python
      •
      GNU General Public License v2.0
      •1•0•7•0•Updated Feb 1, 2026Feb 1, 2026

    • moalmanac-db-jad

      Public
      Underlying content for the Molecular Oncology Almanac's database
      Python
      •
      GNU General Public License v2.0
      •4•0•0•0•Updated Jan 30, 2026Jan 30, 2026

    • snatac-rcc-manuscript

      Public
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jan 30, 2026Jan 30, 2026

    • pnet-simulation

      Public
      Codebase for P-NET (BiNN) simulation paper. Includes P-NET model, and scripts for preprocessing, experiments, and analysis.
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jan 26, 2026Jan 26, 2026

    • moalmanac-browser

      Public
      Web portal interface for browsing the Molecular Oncology Almanac
      pythonflaskmolecular-oncology-almanac
      Python
      •
      GNU General Public License v2.0
      •1•1•8•0•Updated Jan 14, 2026Jan 14, 2026

    • region-specific-approvals-sop

      Public
      An SOP for curating region-specific regulatory approvals
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Jan 9, 2026Jan 9, 2026

    • moalmanac-news

      Public
      News website for the Molecular Oncology Almanac
      molecular-oncology-almanac
      HTML
      •
      GNU General Public License v2.0
      •0•0•1•0•Updated Dec 29, 2025Dec 29, 2025

    • EAC-multiome

      Public
      Jupyter Notebook
      •
      MIT License
      •6•15•0•0•Updated Dec 4, 2025Dec 4, 2025

    • moalmanac-matchmaking

      Public
      Template repository to perform profile-to-cell line matchmaking
      molecular-oncology-almanac
      Python
      •
      GNU General Public License v2.0
      •0•0•3•0•Updated Oct 22, 2025Oct 22, 2025

    • moalmanac-docs

      Public
      Documentation for the Molecular Oncology Almanac
      molecular-oncology-almanac
      GNU General Public License v2.0
      •0•0•0•0•Updated Sep 9, 2025Sep 9, 2025

    • moalmanac-portal

      Public archive
      A cloud-based web portal for accessible clinical interpretation of integrative cancer genomics.
      pythonflaskmolecular-oncology-almanac
      HTML
      •
      GNU General Public License v2.0
      •3•1•3•0•Updated Sep 3, 2025Sep 3, 2025

    • terra-helper

      Public
      Terra storage helper
      Python
      •
      GNU General Public License v2.0
      •0•0•4•1•Updated Sep 3, 2025Sep 3, 2025

    • moalmanac-db-kirtan-summer-2025

      Public archive
      Underlying content for the Molecular Oncology Almanac's database, Canada
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •4•0•0•0•Updated Jul 2, 2025Jul 2, 2025

    • ped_germline_SV

      Public
      Analysis of germline SVs in pediatric cancers
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •1•3•0•0•Updated Apr 30, 2025Apr 30, 2025

    • beanie-analysis

      Public
      Code for reproducing results presented in the BEANIE paper
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Mar 3, 2025Mar 3, 2025

    • beanie

      Public
      Tool for group biology estimation in single-cell RNAseq data
      bioinformaticsscrna-seqsingle-cellrobustnesssubsamplinggene-signaturessignature-scoringdifferential-enrichment
      Python
      •
      GNU General Public License v2.0
      •2•9•0•0•Updated Mar 3, 2025Mar 3, 2025

    • clinicogenomics-FriendsDontLetFriends

      Public
      Directly inspired from Chenxin Li's "Friends Don't Let Friends Make Bad Graphs"
      GNU General Public License v2.0
      •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • germline-somatic-convergence

      Public
      Pilot exploration of overlap between germline and somatic alterations in common adult solid tumors
      R
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

    • chek2_germline

      Public
      Analysis of germline genetic variants in CHEK2
      WDL
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

    • miniconda

      Public
      Dockerfiles for Miniconda
      Dockerfile
      •
      GNU General Public License v2.0
      •1•4•0•0•Updated Nov 5, 2024Nov 5, 2024

    • comut

      Public
      CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots
      Python
      •
      MIT License
      •27•96•10•4•Updated Aug 1, 2024Aug 1, 2024

    • schadendorf-pd1

      Public
      code and data for Liu, Schilling, et al Nat Med 2019
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •6•17•1•0•Updated Aug 1, 2024Aug 1, 2024

    • SigProfilerAssignment-wrapper

      Public
      Implementation repository for SigProfilerAssignment
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jul 12, 2024Jul 12, 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 p…
      paperprecision-cancer-medicinemolecular-oncology-almanac
      HTML
      •
      GNU General Public License v2.0
      •4•5•0•1•Updated Mar 13, 2024Mar 13, 2024

    • pnet

      Public
      Implementation of P-Net as a flexible deep learning tool to generate insights from genetic features.
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •7•9•1•0•Updated Feb 12, 2024Feb 12, 2024

    • microhet-paper

      Public
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•3•0•0•Updated Jan 17, 2024Jan 17, 2024