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    52 repositories

    • RandPedigreePCA

      Public
      Principal Component Analysis of Pedigree Relationship Matrix via Randomized SVD
      Jupyter Notebook
      •3•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • AlphaFamImpute

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

    • AlphaImpute2

      Public
      AlphaImpute2: pedigree- and population-based genotype imputation
      Python
      •
      MIT License
      •6•0•0•0•Updated Oct 29, 2024Oct 29, 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

    • AlphaSimR

      Public
      R package for breeding program simulations
      R
      •
      Other
      •19•0•0•1•Updated Oct 28, 2024Oct 28, 2024

    • 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 15-16th September
      0•4•0•0•Updated Oct 4, 2024Oct 4, 2024

    • jbancic_alphasimr_plants

      Public
      Plant breeding simulations with AlphaSimR
      HTML
      •
      Other
      •8•12•2•0•Updated Sep 19, 2024Sep 19, 2024

    • SIMplyBee

      Public
      SIMplyBee R package extends AlphaSimR for simulating honeybee populations and breeding programmes
      R
      •
      Other
      •6•1•69•1•Updated Sep 19, 2024Sep 19, 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

    • AlphaPart

      Public
      AlphaPart implements a method for partitioning genetic trends to quantify the sources of genetic gain in breeding programmes
      R
      •3•0•0•0•Updated Jul 15, 2024Jul 15, 2024

    • gdejong_gca_with_dominance_models

      Public archive
      Simulation scripts from the study of Guilherme de Jong about genomic prediction with additive and dominance effects in maize breeding
      R
      •1•1•0•0•Updated Jul 15, 2024Jul 15, 2024

    • jbancic_GEIsim

      Public
      This repository contains examples of code for simulating genotype by environment interaction
      R
      •1•4•0•0•Updated Jul 15, 2024Jul 15, 2024

    • gmafrafortuna_mtdna_breed

      Public
      Accounting for nuclear - and mito-genome in dairy cattle breeding: a simulation study
      R
      •0•2•0•0•Updated Jul 11, 2024Jul 11, 2024

    • lstrachan_honeybee_relatedness

      Public
      This repository contain R scripts that demonstrates the principles of expected and realised genetic relatedness among individual honeybees using SIMplyBee.
      R
      •0•0•0•0•Updated May 20, 2024May 20, 2024

    • vpapin_pine_gs

      Public archive
      Simulation of genomic prediction in maritime pine and factors affecting its accuracy
      R
      •1•0•0•0•Updated Dec 31, 2023Dec 31, 2023

    • ipocrnic_OptimisedCore4APY

      Public archive
      Optimisation of the core subset for the APY approximation of genomic relationships
      R
      •
      MIT License
      •0•0•0•0•Updated Nov 22, 2023Nov 22, 2023

    • tinyhouse

      Public
      tinyhouse: Internal (house) functions used across many AlphaGenes tools
      Python
      •6•0•0•0•Updated Oct 16, 2023Oct 16, 2023

    • AlphaPeel

      Public
      AlphaPeel: calling, phasing, and imputing genotype and sequence data in pedigrees
      Roff
      •
      MIT License
      •11•0•0•0•Updated Oct 13, 2023Oct 13, 2023

    • yma_bsf_pop_diff_pool_seq

      Public archive
      Scripts for population genetic differentiation of black soldier fly via pool sequencing
      Shell
      •1•0•0•0•Updated Sep 18, 2023Sep 18, 2023

    • rbsmith_bsf_paternity

      Public archive
      Simulation by RB Smith for evaluating the number of fathers in black soldier flies
      R
      •1•0•0•0•Updated Aug 22, 2023Aug 22, 2023

    • PedigreeToolsF90

      Public
      PedigreeTools.f90 is pedigree cleaning protocol made up of several programmes
      Fortran
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jul 21, 2023Jul 21, 2023

    • nlubanga_tea_breeding_gs

      Public archive
      Simulation of tea breeding programmes using genomic selection
      breedingteaselectiongenomic
      R
      •1•2•0•0•Updated Jul 16, 2023Jul 16, 2023

    • AlphaPlantImpute2

      Public
      AlphaPlantImpute2: Genotype imputation for plant populations
      Python
      •
      MIT License
      •3•0•0•0•Updated Jul 5, 2023Jul 5, 2023

    • toliveira_graphical_ped

      Public
      Pedigree based mixed-effects models using directed acyclic graphs
      HTML
      •1•0•0•0•Updated Jun 6, 2023Jun 6, 2023

    • toliveira_alphapart_variance

      Public archive
      A method for partitioning trends in genetic mean and variance to understand breeding practices
      R
      •0•0•0•0•Updated Jun 5, 2023Jun 5, 2023

    • ipocrnic_Layer_OCS

      Public archive
      Assessment of long-term trends in genetic mean and variance after the introduction of genomic selection in layers: a simulation study
      R
      •
      MIT License
      •0•1•0•0•Updated May 12, 2023May 12, 2023

    • AlphaCMakeFiles

      Public
      CMake
      •1•0•0•0•Updated Feb 12, 2023Feb 12, 2023

    • AlphaHouse

      Public
      Fortran
      •1•0•0•0•Updated Feb 12, 2023Feb 12, 2023

    • AlphaPhase-doc

      Public
      Python
      •1•0•0•0•Updated Feb 12, 2023Feb 12, 2023