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    24 repositories

    • phg_v2

      Public
      Practical Haplotype Graph (PHG) version 2
      imputationpangenomepangenome-graph
      Kotlin
      •
      Apache License 2.0
      •2•21•5•2•Updated Dec 20, 2024Dec 20, 2024

    • biokotlin-tools

      Public
      Command line tools related to BioKotlin
      Kotlin
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 10, 2024Dec 10, 2024

    • rPHG2

      Public
      R interface to PHGv2
      R
      •
      Apache License 2.0
      •0•1•1•0•Updated Dec 10, 2024Dec 10, 2024

    • breeder-genomics-hub

      Public
      The Breeder Genomics Hub is a batteries-included JupyterHub distribution for breeders (Pangeo for plant scientists)
      dockerbioinformaticsjupytergenomicsjupyter-notebookbreedingjupyterhubbrapiplant-sciencephg
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

    • BioKotlin

      Public
      Kotlin
      •
      Apache License 2.0
      •1•6•0•2•Updated Nov 13, 2024Nov 13, 2024

    • rTASSEL

      Public
      R front-end for TASSEL
      gwaslinkage-disequilibriumgenomic-prediction
      R
      •
      Apache License 2.0
      •9•28•0•0•Updated Jul 18, 2024Jul 18, 2024

    • phg-docs

      Public
      0•0•0•0•Updated Jul 9, 2024Jul 9, 2024

    • rPHG

      Public
      R front-end for the Practical Haplotype Graph (PHG)
      R
      •
      Apache License 2.0
      •0•3•0•0•Updated Apr 2, 2024Apr 2, 2024

    • Field-Book

      Public
      Field Book
      Java
      •
      GNU General Public License v2.0
      •54•0•0•0•Updated Mar 19, 2024Mar 19, 2024

    • commonbean-phg-v2

      Public
      Scripts and notes for building a common bean PHG using v2 architecture
      Shell
      •0•0•0•0•Updated Feb 12, 2024Feb 12, 2024

    • hubtools

      Public
      Utility functions designed for R notebooks within the Breeder's Genomics Hub
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Jan 26, 2024Jan 26, 2024

    • bioinformatic_scripts

      Public
      Bioinformatic Scripts written in Kotlin Script, Python, R, etc. that may use BioKotlin, TASSEL 5, TASSEL 6, PHG, etc. as dependencies
      Jupyter Notebook
      •
      GNU Lesser General Public License v2.1
      •0•1•0•0•Updated Nov 29, 2023Nov 29, 2023

    • breeder-notebook

      Public
      A Jupyter Docker Stack for Plant Scientists and Breeders
      pythondockerbioinformaticsrjupytergenomicsjupyter-notebookjupyterhubplant-sciencephg
      Dockerfile
      •
      MIT License
      •0•1•0•0•Updated Aug 29, 2023Aug 29, 2023

    • kotlin-jupyter-libraries

      Public
      Library descriptors for Kotlin kernel for Jupyter
      Apache License 2.0
      •21•0•0•0•Updated Jun 20, 2023Jun 20, 2023

    • reelGeneShiny

      Public
      Shiny App from the hackathon of reelGene scores and other data
      R
      •0•0•0•0•Updated Jun 20, 2023Jun 20, 2023

    • MGJars

      Public
      R package for distributing jar files for rTASSEL and rPHG methods.
      R
      •0•0•0•0•Updated Mar 14, 2023Mar 14, 2023

    • rTASSEL_sandbox

      Public
      rTASSEL sandbox environment using Binder
      Jupyter Notebook
      •1•0•0•0•Updated Jun 3, 2022Jun 3, 2022

    • tassel-6-source

      Public
      Java
      •0•3•0•0•Updated Dec 14, 2021Dec 14, 2021

    • msaR

      Public
      The BioJS MSA viewer wrapped into an R package
      JavaScript
      •11•0•0•0•Updated Sep 22, 2021Sep 22, 2021

    • maize-genetics.github.io

      Public
      Deployment site for test code
      CSS
      •0•0•0•0•Updated Oct 9, 2020Oct 9, 2020

    • kotlin-compiler-server

      Public
      Server for executing kotlin code
      Kotlin
      •
      Apache License 2.0
      •73•0•0•0•Updated Jul 16, 2020Jul 16, 2020

    • bwa-mem2

      Public
      The next version of bwa-mem
      C++
      •
      Other
      •102•1•0•0•Updated Jul 13, 2020Jul 13, 2020

    • models

      Public
      Model zoo for genomics
      Python
      •
      MIT License
      •60•0•0•0•Updated Sep 9, 2019Sep 9, 2019

    • bioconductor_test

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 5, 2019Aug 5, 2019