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@Atkinson-Lab The Atkinson Lab at Baylor College of Medicine

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    13 repositories

    • Nextflow_GWAS_pipeline

      Public
      a nextflow pipeline to allow optional selection of various GWAS tools using a population-stratified approach followed by MR-MEGA or MR-MEGA-env meta-analysis
      Nextflow
      •1•0•0•1•Updated Sep 2, 2026Sep 2, 2026

    • MIDreference

      Public
      Scripts for genomic data harmonization, label-agnostic visualization, and inferring genetic ancestry.
      HTML
      •0•1•0•0•Updated Sep 1, 2026Sep 1, 2026

    • TractorWorkflow

      Public
      Nextflow pipeline for Tractor GWAS with customizable phasing, local ancestry inference (RFMix2, GNomix, FLARE), and regression modules.
      Nextflow
      •
      MIT License
      •3•2•0•2•Updated Jul 30, 2026Jul 30, 2026

    • Tractor

      Public
      Scripts for implementing the Tractor pipeline
      tractorgwas-modeltractor-pipeline
      tractorgwas-modeltractor-pipeline
      Jupyter Notebook
      •
      MIT License
      •16•59•8•3•Updated Jul 29, 2026Jul 29, 2026

    • Tractor-Burden

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Jul 16, 2026Jul 16, 2026

    • Tractor-Burden-Simulations-Summary-Stats

      Public
      0•0•0•0•Updated Jun 24, 2026Jun 24, 2026

    • Tractor-PGS

      Public
      Polygenic score model leveraging Tractor framework
      0•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • PGS_Array_WGS

      Public
      Scripts for PGS analyses in the paper
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated Mar 3, 2026Mar 3, 2026

    • Tractor-tutorial

      Public
      A tutorial for running Tractor and Tractor-Mix on toy datasets, including step-by-step instructions for preparing data, estimating PCs and GRMs, and performing …
      Jupyter Notebook
      •4•13•0•0•Updated Dec 22, 2025Dec 22, 2025

    • Tractor-Mix

      Public
      The source code for Tractor-Mix
      R
      •
      MIT License
      •2•5•2•0•Updated Dec 22, 2025Dec 22, 2025

    • LAI-sims-accuracy

      Public
      Code for determining local ancestry inference accuracy
      Shell
      •
      MIT License
      •0•1•0•0•Updated Aug 5, 2025Aug 5, 2025

    • Tractor-Mix-manuscript

      Public
      Scripts for running simulations, and Tractor-Mix analysis for UKBB, and Yale-Penn cohort
      HTML
      •0•0•0•0•Updated May 19, 2025May 19, 2025

    • Post-QC

      Public
      Post variant-calling QC pipeline for orienting cohort data with a reference file. Additional steps for merging and phasing with a reference panel.
      Python
      •5•12•1•0•Updated Jun 10, 2019Jun 10, 2019
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