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    71 repositories

    • RcppTskit

      Public
      R access to the tskit C API
      C
      •5•3•15•1•Updated Aug 20, 2026Aug 20, 2026

    • AlphaPeel

      Public
      AlphaPeel: calling, phasing, and imputing genotype and sequence data in pedigrees
      Python
      •
      MIT License
      •12•0•0•0•Updated Aug 7, 2026Aug 7, 2026

    • AlphaImpute2

      Public
      AlphaImpute2: pedigree- and population-based genotype imputation
      Python
      •
      MIT License
      •9•0•0•0•Updated Aug 7, 2026Aug 7, 2026

    • lstrachan_patrilines

      Public
      This repository contain R scripts that TODO
      R
      •1•0•1•0•Updated Jun 24, 2026Jun 24, 2026

    • tinyhouse

      Public
      tinyhouse: Internal (house) functions used across many AlphaGenes tools
      Python
      •7•0•0•0•Updated Jun 13, 2026Jun 13, 2026

    • mirror_repositories

      Public
      0•0•0•0•Updated May 12, 2026May 12, 2026

    • AlphaSimR

      Public
      R package for breeding program simulations
      R
      •
      Other
      •29•0•16•2•Updated May 4, 2026May 4, 2026

    • shiny-k-mers

      Public
      Tetemer, an R package and Shiny app for interactively fitting population parameters to k-mer spectra of diploids, triploids, and tetraploids (allo and auto)
      R
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Apr 27, 2026Apr 27, 2026

    • AlphaFamImpute

      Public
      Python
      •
      MIT License
      •2•1•0•0•Updated Apr 20, 2026Apr 20, 2026

    • AlphaAssign

      Public
      Roff
      •
      MIT License
      •2•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • AlphaPart

      Public
      AlphaPart implements a method for partitioning genetic trends to quantify the sources of genetic gain in breeding programmes
      R
      •4•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • RcppTskitTestLinking

      Public
      R
      •
      Other
      •0•1•1•0•Updated Mar 2, 2026Mar 2, 2026

    • yzhang_stdpopsim_pig_recomb

      Public
      Formatting genetic map (recombination rate map) for pig species in stdpopsim
      Jupyter Notebook
      •1•0•0•0•Updated Feb 25, 2026Feb 25, 2026

    • highlanderlab.r-universe.dev

      Public
      R universe for packages from the HighlanderLab and friends
      0•0•0•0•Updated Feb 4, 2026Feb 4, 2026

    • SheepTreeSeq

      Public
      Simulation code etc.
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Feb 3, 2026Feb 3, 2026

    • ihouaga_adgg_spatial

      Public
      Scripts for spatial modelling of the ADGG data
      R
      •0•0•0•0•Updated Jan 24, 2026Jan 24, 2026

    • EUCARPIA2025BiometricsPlantBreeding

      Public
      This is a repository hosting public information about the EUCARPIA 2025 Biometrics in Plant Breeding in Edinburgh 17-19th September 2025 + Satellite workshop 15…
      Ruby
      •2•5•0•0•Updated Jan 5, 2026Jan 5, 2026

    • gmafrafortuna_mtdna_breed

      Public
      Accounting for nuclear - and mito-genome in dairy cattle breeding: a simulation study
      R
      •0•2•1•0•Updated Dec 9, 2025Dec 9, 2025

    • SIMplyBee

      Public
      SIMplyBee R package extends AlphaSimR for simulating honeybee populations and breeding programmes
      R
      •
      Other
      •6•3•67•1•Updated Nov 20, 2025Nov 20, 2025

    • hbecher_ASR2kmerGwas

      Public
      Code to convert ASR simulations to k-mer datasets
      R
      •
      MIT License
      •0•0•0•0•Updated Nov 6, 2025Nov 6, 2025

    • RandPedPCA

      Public
      Principal Component Analysis of Pedigree Relationship Matrix via Randomized SVD
      Jupyter Notebook
      •5•7•8•0•Updated Oct 10, 2025Oct 10, 2025

    • amartin_born2guide_seq

      Public
      Script for the simulation reported on paper ... DOI:
      R
      •2•0•0•0•Updated Oct 6, 2025Oct 6, 2025

    • gmafrafortuna_quangen_tree

      Public
      Scripts for quantitative genetic analyses leveraging genome sequence context
      R
      •
      GNU General Public License v3.0
      •1•2•0•0•Updated Sep 9, 2025Sep 9, 2025

    • santonios_sheep_idl

      Public
      Project on evaluating the estimation of inbreeding load in dairy sheep and selecting against it
      R
      •1•0•0•0•Updated Sep 5, 2025Sep 5, 2025

    • almondsim

      Public
      Almond breeding simulations with AlphaSimR
      R
      •
      Other
      •18•0•0•0•Updated Aug 25, 2025Aug 25, 2025

    • idecarlos_honeybee_import

      Public
      Simulation of honeybee imports by Irene de Carlos
      R
      •0•0•0•0•Updated Apr 23, 2025Apr 23, 2025

    • AlphaPhase

      Public
      Fortran
      •
      MIT License
      •2•0•0•0•Updated Apr 2, 2025Apr 2, 2025

    • RobustOCS

      Public
      Robust optimal contribution selection problems for genetics with Python
      Python
      •
      MIT License
      •3•0•0•0•Updated Mar 25, 2025Mar 25, 2025

    • vpapin_pine_gs

      Public archive
      Simulation of genomic prediction in maritime pine and factors affecting its accuracy
      R
      •1•2•0•0•Updated Mar 7, 2025Mar 7, 2025

    • svanvanhossou_africross

      Public
      R
      •1•0•0•0•Updated Feb 20, 2025Feb 20, 2025
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