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    28 repositories

    • ichorCNA_WDL

      Public
      Has Dockerfile and WDL pipeline for ichorCNA
      WDL
      •
      BSD 3-Clause Clear License
      •0•1•0•0•Updated Nov 27, 2024Nov 27, 2024

    • ichorCNA

      Public
      Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
      R
      •
      GNU General Public License v3.0
      •89•14•11•0•Updated Nov 22, 2024Nov 22, 2024

    • GavinHaLab.github.io

      Public
      Gavin Ha Lab Website
      JavaScript
      •0•1•0•3•Updated Nov 15, 2024Nov 15, 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

    • PEARL

      Public
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • TitanCNA_SV_WGS

      Public
      R
      •
      MIT License
      •1•1•0•2•Updated Sep 3, 2024Sep 3, 2024

    • Keraon

      Public
      A tool for estimating heterogenous phenotype fractions from ctDNA features
      Python
      •
      Other
      •2•1•0•0•Updated Jun 6, 2024Jun 6, 2024

    • CDK12-CRPC-paper

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

    • CRPCSubtypingPaper

      Public
      Analysis code used in ctDNA CRPC phenotype manuscript
      Python
      •
      Other
      •1•2•2•0•Updated May 24, 2024May 24, 2024

    • WDL-Pipelines

      Public
      A central repository for tools wrapped in WDL for the Ha lab.
      WDL
      •0•0•1•0•Updated May 23, 2024May 23, 2024

    • TritonNP

      Public
      A tool for extracting region-based phasing features from cell-free DNA
      Python
      •
      Other
      •2•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

    • Admixtures_snakemake

      Public
      Python
      •0•0•0•0•Updated Nov 17, 2023Nov 17, 2023

    • Griffin

      Public
      A flexible framework for nucleosome profiling of cell-free DNA
      Python
      •
      Other
      •16•6•0•0•Updated Aug 25, 2023Aug 25, 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

    • mutect2_snakemake

      Public
      A snakemake to run Mutect2 on analysis-ready bams, following GATK best practices.
      3•1•0•0•Updated Jan 10, 2022Jan 10, 2022

    • PDX_mouseSubtraction

      Public
      Shell
      •0•2•0•0•Updated Jan 10, 2022Jan 10, 2022

    • ichorCNA_SV_WGS_tumorOnly

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

    • SV_WGS_analysis

      Public
      Structural variation analysis pipeline for cancer genomes
      R
      •
      MIT License
      •1•5•1•0•Updated Jan 10, 2022Jan 10, 2022

    • SV_10X_analysis

      Public
      Structural variation analysis of 10X Genomics linked-read data
      R
      •
      MIT License
      •4•5•0•0•Updated Jan 10, 2022Jan 10, 2022

    • pdx_evolution_study

      Public
      This repository contains the scripts and data needed to reproduce the findings of our PDX evolution study.
      Python
      •2•2•0•0•Updated Sep 13, 2021Sep 13, 2021

    • TitanCNA_SV_WGS_tumorOnly

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 23, 2021Apr 23, 2021

    • ichorCNA_offtarget

      Public
      Estimating tumor fraction by exploiting the off-target reads from targeted DNA sequencing.
      R
      •
      MIT License
      •4•6•0•0•Updated Feb 16, 2021Feb 16, 2021

    • TitanCNA_10X_snakemake

      Public
      Snakemake workflow for 10X Genomics WGS analysis using TitanCNA
      R
      •
      MIT License
      •4•5•6•0•Updated Feb 16, 2021Feb 16, 2021

    • Sequencing_analysis_assignment

      Public
      Sequencing analysis questions
      MIT License
      •2•0•0•0•Updated Jun 29, 2019Jun 29, 2019