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    66 repositories

    • RcppTskit

      Public
      R access to the tskit C API
      C
      •5•3•22•1•Updated Apr 10, 2026Apr 10, 2026

    • AlphaSimR

      Public
      R package for breeding program simulations
      R
      •
      Other
      •27•0•14•0•Updated Apr 3, 2026Apr 3, 2026

    • RcppTskitTestLinking

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

    • AlphaPeel

      Public
      AlphaPeel: calling, phasing, and imputing genotype and sequence data in pedigrees
      Python
      •
      MIT License
      •12•0•0•0•Updated Feb 27, 2026Feb 27, 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

    • tinyhouse

      Public
      tinyhouse: Internal (house) functions used across many AlphaGenes tools
      Python
      •7•0•0•0•Updated Feb 5, 2026Feb 5, 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

    • 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

    • AlphaImpute2

      Public
      AlphaImpute2: pedigree- and population-based genotype imputation
      Python
      •
      MIT License
      •9•0•0•0•Updated Dec 4, 2025Dec 4, 2025

    • SIMplyBee

      Public
      SIMplyBee R package extends AlphaSimR for simulating honeybee populations and breeding programmes
      R
      •
      Other
      •6•3•62•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•6•10•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
      •19•0•0•0•Updated Aug 25, 2025Aug 25, 2025

    • lstrachan_patrilines

      Public
      This repository contain R scripts that TODO
      R
      •1•0•1•0•Updated Aug 22, 2025Aug 22, 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

    • 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

    • 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 Feb 23, 2025Feb 23, 2025

    • svanvanhossou_africross

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

    • jbancic_alphasimr_plants

      Public
      Plant breeding simulations with AlphaSimR
      HTML
      •
      Other
      •19•27•1•0•Updated Jan 5, 2025Jan 5, 2025

    • irebollo_rice_tree

      Public
      Scripts for genomic prediction and association studies using tree sequence in rice
      R
      •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • AlphaFamImpute

      Public
      Python
      •
      MIT License
      •2•1•0•0•Updated Nov 15, 2024Nov 15, 2024

    • vbrajkovic_cattle_mtdna

      Public
      Analysis of the effect of mtDNA on dairy cattle performance
      R
      •
      MIT License
      •0•1•0•0•Updated Oct 28, 2024Oct 28, 2024

    • sheep_ts_demo

      Public
      HTML
      •
      MIT License
      •1•0•0•0•Updated Sep 9, 2024Sep 9, 2024

    • tree_seq_pipeline

      Public
      Pipeline to infer tree sequences with different datasets
      Python
      •
      MIT License
      •7•3•15•1•Updated Jul 26, 2024Jul 26, 2024
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