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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 18 13

  2. WDL-Pipelines WDL-Pipelines Public

    A central repository for tools wrapped in WDL for the Ha lab.

    WDL

  3. Griffin Griffin Public

    Forked from adoebley/Griffin

    A flexible framework for nucleosome profiling of cell-free DNA

    Python 8 5

  4. PEARL PEARL Public

    Jupyter Notebook 3

  5. Keraon Keraon Public

    Forked from denniepatton/Keraon

    A tool for estimating heterogenous phenotype fractions from ctDNA features

    Python 1

  6. TitanCNA_SV_WGS TitanCNA_SV_WGS Public

    R 1 1

Repositories

Showing 10 of 35 repositories
  • 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 0 1 0 0 Updated Jan 22, 2026
  • GavinHaLab.github.io Public

    Gavin Ha Lab Website

    GavinHaLab/GavinHaLab.github.io’s past year of commit activity
    JavaScript 1 0 0 3 Updated Jan 7, 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 18 GPL-3.0 96 12 2 Updated Dec 9, 2025
  • TitanCNA_SV_WGS Public
    GavinHaLab/TitanCNA_SV_WGS’s past year of commit activity
    R 1 MIT 1 0 3 Updated Oct 27, 2025
  • 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 0 0 0 Updated Oct 7, 2025
  • PEARL Public
    GavinHaLab/PEARL’s past year of commit activity
    Jupyter Notebook 3 0 2 0 Updated Sep 17, 2025
  • 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 Sep 10, 2025
  • 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 Sep 9, 2025
  • 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 Aug 28, 2025
  • BLCA-subtype-evolution-paper Public
    GavinHaLab/BLCA-subtype-evolution-paper’s past year of commit activity
    Python 0 0 0 0 Updated Aug 21, 2025
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