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@Atkinson-Lab

The Atkinson Lab at Baylor College of Medicine

Code created by the Atkinson lab at Baylor College of Medicine lives here. We work on population and statistical genomics across diverse populations.

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  1. Tractor Tractor Public

    Scripts for implementing the Tractor pipeline

    Jupyter Notebook 55 14

  2. Tractor-tutorial 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 mixed-model association tests.

    Jupyter Notebook 11 4

Repositories

Showing 9 of 9 repositories
  • PGS_Array_WGS Public

    Scripts for PGS analyses in the paper

    Atkinson-Lab/PGS_Array_WGS’s past year of commit activity
    Jupyter Notebook 2 MIT 1 0 0 Updated Mar 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 mixed-model association tests.

    Atkinson-Lab/Tractor-tutorial’s past year of commit activity
    Jupyter Notebook 11 4 0 0 Updated Dec 22, 2025
  • Tractor-Mix Public

    The source code for Tractor-Mix

    Atkinson-Lab/Tractor-Mix’s past year of commit activity
    R 1 MIT 1 0 0 Updated Dec 22, 2025
  • Nextflow_GWAS_pipeline Public Forked from chrisrob3312/Nextflow_GWAS_pipeline

    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

    Atkinson-Lab/Nextflow_GWAS_pipeline’s past year of commit activity
    Nextflow 0 1 0 0 Updated Dec 12, 2025
  • TractorWorkflow Public

    Nextflow pipeline for Tractor GWAS with customizable phasing, local ancestry inference (RFMix2, GNomix, FLARE), and regression modules.

    Atkinson-Lab/TractorWorkflow’s past year of commit activity
    Nextflow 2 MIT 3 0 2 Updated Nov 24, 2025
  • Tractor Public

    Scripts for implementing the Tractor pipeline

    Atkinson-Lab/Tractor’s past year of commit activity
    Jupyter Notebook 55 MIT 14 7 3 Updated Sep 4, 2025
  • LAI-sims-accuracy Public

    Code for determining local ancestry inference accuracy

    Atkinson-Lab/LAI-sims-accuracy’s past year of commit activity
    Shell 1 MIT 0 0 0 Updated Aug 5, 2025
  • Tractor-Mix-manuscript Public

    Scripts for running simulations, and Tractor-Mix analysis for UKBB, and Yale-Penn cohort

    Atkinson-Lab/Tractor-Mix-manuscript’s past year of commit activity
    HTML 0 0 0 0 Updated May 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.

    Atkinson-Lab/Post-QC’s past year of commit activity
    Python 11 5 1 0 Updated Jun 10, 2019

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