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    23 repositories

    • popgenml

      Public
      Repository for simulating population genetic data and training neural networks to do inference.
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • TEforest

      Public
      Finding TEs with short-read data using random forests
      R
      •
      MIT License
      •1•9•1•0•Updated Mar 16, 2026Mar 16, 2026

    • Detecting_Selection_Aedes_Aegypti_2026

      Public
      Shell
      •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • geneConvSweeps

      Public
      Code for simulation study exaiming the impact of gene conversion on the "softness" of selective sweeps
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 9, 2026Jan 9, 2026

    • TreeSeqPopGenInference

      Public
      Exploring how to use tree sequences for multiple population genetic inference tasks.
      Shell
      •
      Other
      •2•1•0•0•Updated Aug 4, 2025Aug 4, 2025

    • cancer_sims

      Public
      Slim
      •
      MIT License
      •1•0•0•0•Updated Jun 11, 2025Jun 11, 2025

    • simscale-snakemake

      Public
      Snakemake pipeline for parsing simulation outputs across scaling factors
      Python
      •
      MIT License
      •0•2•0•0•Updated Sep 18, 2024Sep 18, 2024

    • selectionScanExercise

      Public
      HTML
      •1•1•0•0•Updated May 22, 2024May 22, 2024

    • evoMLWorkshop2024

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated May 17, 2024May 17, 2024

    • Timesweeper

      Public
      Python package for detecting positive selective sweeps using time-series genomics sampling data.
      geneticsneural-networksconvolutional-neural-networks
      geneticsneural-networksconvolutional-neural-networkspopulation-genomicspopulation-genetics
      Python
      •
      MIT License
      •2•19•6•0•Updated Apr 9, 2024Apr 9, 2024

    • PG-Alignments-GAN

      Public
      Generative Adversarial Network (GAN) of Population Genetic Alignments
      Python
      •1•3•0•0•Updated Feb 21, 2024Feb 21, 2024

    • introNets

      Public
      Python
      •
      GNU General Public License v3.0
      •1•5•3•0•Updated Feb 2, 2024Feb 2, 2024

    • timesweeper-experiments

      Public
      Repo for experiments for the TimeSweeper manuscript.
      Jupyter Notebook
      •
      MIT License
      •1•5•0•0•Updated May 9, 2023May 9, 2023

    • permEnrichmentTest

      Public
      Some scripts for doing permutation-based enrichment tests
      Python
      •0•0•0•0•Updated Jul 26, 2022Jul 26, 2022

    • GeneGraphs

      Public
      Repo for generating genetic trees from specified demographic models and running predictions via PyTorch Geometric
      Python
      •0•1•0•0•Updated Jun 14, 2022Jun 14, 2022

    • drosophila_phylogeny

      Public
      Pipeline overview and code (including BLT-DCT program) for widespread introgression across a phylogeny of 155 Drosophila genomes
      R
      •1•8•1•0•Updated Nov 14, 2021Nov 14, 2021

    • ArtificialGenes

      Public
      Using generative networks to create sequences of artificial DNA
      Jupyter Notebook
      •0•0•0•0•Updated Sep 24, 2021Sep 24, 2021

    • sim_scaling

      Public
      Slim
      •0•0•0•0•Updated Jul 21, 2021Jul 21, 2021

    • CancerSim

      Public
      Slim
      •0•0•0•0•Updated May 4, 2021May 4, 2021

    • intro_UNET

      Public
      UNET for semantic segmentation of SNP data.
      Python
      •0•0•0•0•Updated Mar 15, 2021Mar 15, 2021

    • posSelVsBgs

      Public
      Simulations comparing expected patterns of variation under hitchhiking and BGS models in human/drosophila genomes
      Python
      •0•0•0•0•Updated Jun 21, 2020Jun 21, 2020

    • dfoil

      Public
      DFOIL: Introgression Testing for Five Taxa
      Python
      •
      GNU General Public License v3.0
      •11•0•0•0•Updated Mar 19, 2020Mar 19, 2020

    • Tree_learning

      Public
      Code for accurate inference of tree topologies from multiple sequence alignments using deep learning
      R
      •1•10•0•0•Updated Nov 3, 2019Nov 3, 2019
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