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    19 repositories

    • ML-MAGES

      Public
      ML-MAGES: Machine learning approaches for multivariate genetic association analyses with genes and effect size shrinkage
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • SWIFr

      Public
      Sweep Inference Framework (controlling for correlation)
      OpenEdge ABL
      •
      GNU General Public License v3.0
      •4•29•1•27•Updated Jul 10, 2024Jul 10, 2024

    • multiancestry_enrichment

      Public
      Example code and scripts for Smith et al. 2022
      OpenEdge ABL
      •
      Creative Commons Zero v1.0 Universal
      •0•2•0•0•Updated May 6, 2024May 6, 2024

    • archaic-chrX-sexbias

      Public
      Code and data to reproduce main figures and simulations of Chevy, Huerta-Sanchez, and Ramachandran, 202X
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Apr 30, 2024Apr 30, 2024

    • resources

      Public
      Best practices and scientific resources
      0•0•0•0•Updated Feb 24, 2023Feb 24, 2023

    • SRS_paper

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 15, 2022Nov 15, 2022

    • ESNN

      Public
      Code and simulations using an Ensemble of Single-Effect Neural Networks (ESNN)
      gwasgeneticsvariable-selectionneural-networksbayesian-statisticsinterpretabilitygwas-toolsmachine-learning
      Python
      •
      MIT License
      •1•5•0•0•Updated Nov 11, 2022Nov 11, 2022

    • deceptive_deeppath

      Public
      Python
      •0•0•0•0•Updated Jun 22, 2022Jun 22, 2022

    • pong

      Public
      Fast analysis and visualization of latent clusters in population genetic data
      Python
      •12•68•0•1•Updated Mar 29, 2022Mar 29, 2022

    • UPD_Detector

      Public
      code and classifier parameters for ROH-based UPD detection
      R
      •0•1•0•0•Updated Jan 26, 2021Jan 26, 2021

    • HEBAE

      Public
      Code and Analyses using the Hierarchical Empirical Bayes Autoencoder (HEBAE)
      machine-learningautoencodervariational-inferencevariational-autoencoderempirical-bayes
      Python
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Jul 29, 2020Jul 29, 2020

    • PEGASUS_flies

      Public
      Application of the PEGASUS gene-level association test to the Drosophila Genome Reference Panel
      Perl
      •0•0•0•0•Updated Jul 10, 2020Jul 10, 2020

    • genee

      Public
      An Association Test for Aggregated Sets of SNP-Level Summary Statistics
      R
      •
      MIT License
      •1•7•1•0•Updated Jun 25, 2020Jun 25, 2020

    • ARG_Symposium

      Public
      Dates: January 8, 9, 10, 13, 14, 15
      0•0•0•0•Updated Jan 10, 2020Jan 10, 2020

    • PEGASUS-WINGS

      Public
      gwasgeneticsclustering
      MATLAB
      •
      Other
      •1•4•0•0•Updated May 18, 2019May 18, 2019

    • PEGASUS

      Public
      Scripts and references files for PEGASUS software for calculating gene-level p-values from GWA p-values
      Perl
      •2•4•0•0•Updated Dec 6, 2018Dec 6, 2018

    • soft-sweeps-dev-v2

      Public
      Python
      •0•1•0•0•Updated Apr 1, 2018Apr 1, 2018

    • MixedAncestryGenomics

      Public
      Course Materials for Biol 2440, Spring 2018
      0•2•0•0•Updated Feb 9, 2018Feb 9, 2018

    • public_workflow_test

      Public
      0•0•0•0•Updated Aug 22, 2016Aug 22, 2016