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@GavinHaLab

GavinHaLab

Cancer Genomics and Computational Biology Lab at Fred Hutch

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  1. ichorCNA ichorCNA Public

    Forked from broadinstitute/ichorCNA

    Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

    R 22 15

  2. Griffin Griffin Public

    Forked from adoebley/Griffin

    A flexible framework for nucleosome profiling of cell-free DNA

    Python 10 6

  3. PEARL PEARL Public

    Jupyter Notebook 4 2

  4. Keraon Keraon Public

    Forked from denniepatton/Keraon

    A tool for estimating heterogenous phenotype fractions from ctDNA features

    Python 1

  5. TitanCNA_SV_WGS TitanCNA_SV_WGS Public

    R 1 1

Repositories

Showing 10 of 36 repositories
  • GavinHaLab.github.io Public

    Gavin Ha Lab Website

    GavinHaLab/GavinHaLab.github.io's past year of commit activity
    JavaScript 1 0 0 3 Updated Oct 8, 2026
  • titancna-curation-agent Public

    No-API-lock-in CLI agent that curates TitanCNA copy-number/LOH candidate solutions using independent Claude + Gemini visual review.

    GavinHaLab/titancna-curation-agent's past year of commit activity
    Python 0 MIT 0 0 0 Updated Oct 3, 2026
  • TitanCNA_SV_WGS Public
    GavinHaLab/TitanCNA_SV_WGS's past year of commit activity
    R 1 MIT 1 0 3 Updated Sep 16, 2026
  • ichorCNA Public Forked from broadinstitute/ichorCNA

    Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

    GavinHaLab/ichorCNA's past year of commit activity
    R 22 GPL-3.0 106 14 6 Updated Sep 15, 2026
  • Triton Public Forked from denniepatton/Triton

    As a cell-free DNA (cfDNA) processing pipeline, Triton conducts fragmentomic and phased-nucleosome coverage analyses on individual or composite genomic regions and outputs both region-level biomarkers and nt-resolution signal profiles.

    GavinHaLab/Triton's past year of commit activity
    Python 6 1 0 0 Updated Jun 12, 2026
  • BLCA-subtype-evolution-paper Public
    GavinHaLab/BLCA-subtype-evolution-paper's past year of commit activity
    Python 2 0 0 0 Updated May 7, 2026
  • ichorCNA_WDL Public

    Has Dockerfile and WDL pipeline for ichorCNA

    GavinHaLab/ichorCNA_WDL's past year of commit activity
    WDL 1 BSD-3-Clause-Clear 0 0 0 Updated May 6, 2026
  • mutect2_snakemake Public Forked from annahoge/mutect2_snakemake

    A snakemake to run Mutect2 on analysis-ready bams, following GATK best practices.

    GavinHaLab/mutect2_snakemake's past year of commit activity
    Python 1 3 0 0 Updated Mar 24, 2026
  • Keraon Public Forked from denniepatton/Keraon

    A tool for estimating heterogenous phenotype fractions from ctDNA features

    GavinHaLab/Keraon's past year of commit activity
    Python 1 2 0 0 Updated Mar 4, 2026
  • CRAMboozle Public

    A snakemake workflow for CRAMboozle on Fred Hutch servers. CRAMboozle is a modified version of BAMboozle which de-identifies alignment data and takes either BAM or CRAM format for both input and output (CRAM to CRAM by default).

    GavinHaLab/CRAMboozle's past year of commit activity
    Python 0 GPL-3.0 1 0 0 Updated Mar 3, 2026
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