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    36 repositories

    • titancna-curation-agent

      Public
      No-API-lock-in CLI agent that curates TitanCNA copy-number/LOH candidate solutions using independent Claude + Gemini visual review.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 1, 2026Oct 1, 2026

    • GavinHaLab.github.io

      Public
      Gavin Ha Lab Website
      JavaScript
      •0•1•0•3•Updated Sep 17, 2026Sep 17, 2026

    • TitanCNA_SV_WGS

      Public
      R
      •
      MIT License
      •1•1•0•3•Updated Sep 17, 2026Sep 17, 2026

    • ichorCNA

      Public
      Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
      R
      •
      GNU General Public License v3.0
      •103•21•13•3•Updated Sep 15, 2026Sep 15, 2026

    • Triton

      Public
      As a cell-free DNA (cfDNA) processing pipeline, Triton conducts fragmentomic and phased-nucleosome coverage analyses on individual or composite genomic regions …
      Python
      •
      Other
      •1•5•0•0•Updated Jun 12, 2026Jun 12, 2026

    • BLCA-subtype-evolution-paper

      Public
      Python
      •
      Other
      •0•2•0•0•Updated May 7, 2026May 7, 2026

    • ichorCNA_WDL

      Public
      Has Dockerfile and WDL pipeline for ichorCNA
      WDL
      •
      BSD 3-Clause Clear License
      •0•1•0•0•Updated May 6, 2026May 6, 2026

    • mutect2_snakemake

      Public
      A snakemake to run Mutect2 on analysis-ready bams, following GATK best practices.
      Python
      •3•1•0•0•Updated Mar 24, 2026Mar 24, 2026

    • Keraon

      Public
      A tool for estimating heterogenous phenotype fractions from ctDNA features
      Python
      •
      Other
      •2•1•0•0•Updated Mar 4, 2026Mar 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…
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 3, 2026Mar 3, 2026

    • PEARL

      Public
      Jupyter Notebook
      •
      Other
      •2•4•2•1•Updated Sep 17, 2025Sep 17, 2025

    • LNCaP-subline-paper

      Public
      Code, scripts, data for analyses presented in
      Python
      •
      Other
      •0•0•0•0•Updated Aug 6, 2025Aug 6, 2025

    • CRPC-docetaxel-cfDNA-paper

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • Admixtures_snakemake_WGSMetrics

      Public
      Python
      •0•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • ichorCurate

      Public
      A solution curation application to supplement ichorCNA
      Python
      •
      Other
      •2•0•0•0•Updated Jun 23, 2025Jun 23, 2025

    • Admixtures_snakemake

      Public
      Python
      •0•0•0•1•Updated Jun 13, 2025Jun 13, 2025

    • Griffin

      Public
      A flexible framework for nucleosome profiling of cell-free DNA
      Python
      •
      Other
      •23•10•0•1•Updated May 12, 2025May 12, 2025

    • Sequencing_analysis_assignment

      Public
      Sequencing analysis questions
      MIT License
      •2•0•0•0•Updated Apr 1, 2025Apr 1, 2025

    • WDL-Pipelines

      Public
      A central repository for tools wrapped in WDL for the Ha lab.
      WDL
      •0•0•1•0•Updated Feb 1, 2025Feb 1, 2025

    • CRPCSubtypingPaper

      Public
      Analysis code used in ctDNA CRPC phenotype manuscript
      Python
      •
      Other
      •1•5•2•0•Updated Dec 6, 2024Dec 6, 2024

    • crpc-sv-pattern-study

      Public
      R
      •3•2•0•0•Updated Nov 14, 2024Nov 14, 2024

    • fastq_to_bam_paired_snakemake

      Public
      A snakemake to convert paired fastq files to analysis-ready bams, following GATK best practices.
      Python
      •4•1•0•0•Updated Oct 3, 2024Oct 3, 2024

    • CDK12-CRPC-paper

      Public
      R
      •
      BSD 3-Clause Clear License
      •0•0•0•0•Updated May 28, 2024May 28, 2024

    • TritonNP

      Public
      A tool for extracting region-based phasing features from cell-free DNA
      Python
      •
      Other
      •3•0•0•0•Updated Apr 23, 2024Apr 23, 2024

    • SCLCpheno-seq_paper

      Public
      Jupyter Notebook
      •
      Other
      •0•1•0•0•Updated Nov 20, 2023Nov 20, 2023

    • gridss2_somatic_sv_call

      Public
      R
      •0•0•0•1•Updated Jun 21, 2023Jun 21, 2023

    • downsampling_snakemake

      Public
      2•0•0•0•Updated Feb 7, 2022Feb 7, 2022

    • fastq_to_bam_interleaved_snakemake

      Public
      A snakemake to convert interleaved fastq files to analysis-ready bams, following GATK best practices.
      1•0•0•0•Updated Jan 10, 2022Jan 10, 2022

    • PDX_mouseSubtraction

      Public
      Shell
      •0•3•0•0•Updated Jan 10, 2022Jan 10, 2022

    • ichorCNA_SV_WGS_tumorOnly

      Public
      R
      •1•3•0•0•Updated Jan 10, 2022Jan 10, 2022
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