Repositories list

• MLImpute

  Public
  Simple tool to run Machine Learning based imputation techniques

  Python

  •

  Apache License 2.0

  •0•0•10•1•Updated Aug 19, 2025Aug 19, 2025

• phg_v2

  Public
  Practical Haplotype Graph (PHG) version 2

  imputationpangenomepangenome-graph

  Kotlin

  •

  Apache License 2.0

  •2•27•12•3•Updated Aug 18, 2025Aug 18, 2025

• poaceae_tfbs

  Public
  Evolution of cis-regulatory motifs across 589 grass species

  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Aug 14, 2025Aug 14, 2025

• tassel

  Public
  Trait Analysis by aSSociation, Evolution and Linkage

  gwaslinkage-disequilibriumimputation+ 1quantitative-genetics

  Java

  •1•0•0•0•Updated Aug 1, 2025Aug 1, 2025

• tassel_test_data

  Public
  Repo for housing TASSEL testing data

  0•0•0•0•Updated Jun 4, 2025Jun 4, 2025

• biokotlin-tools

  Public
  Command line tools related to BioKotlin

  Kotlin

  •

  Apache License 2.0

  •0•2•1•0•Updated Jun 3, 2025Jun 3, 2025

• BioKotlin

  Public
  High performance bioinformatics library for Kotlin

  bioinformaticssequence-manipulationgenomics-analysis

  Kotlin

  •

  Apache License 2.0

  •1•7•0•2•Updated Jun 2, 2025Jun 2, 2025

• rtassel_docker

  Public
  Docker image for rTASSEL

  Dockerfile

  •0•0•0•0•Updated May 2, 2025May 2, 2025

• rTASSEL

  Public
  R front-end for TASSEL 5

  gwaslinkage-disequilibriumgenomic-prediction

  R

  •

  Apache License 2.0

  •9•31•0•0•Updated Apr 23, 2025Apr 23, 2025

• rPHG2

  Public
  R interface to PHGv2

  R

  •

  Apache License 2.0

  •0•2•1•0•Updated Feb 26, 2025Feb 26, 2025

• rPHG

  Public
  R front-end for the Practical Haplotype Graph (PHG)

  R

  •

  Apache License 2.0

  •0•3•0•0•Updated Feb 26, 2025Feb 26, 2025

• breeder-genomics-hub

  Public
  The Breeder Genomics Hub is a batteries-included JupyterHub distribution for breeders (Pangeo for plant scientists)

  dockerbioinformaticsjupyter+ 7genomicsjupyter-notebookbreedingjupyterhubbrapiplant-sciencephg

  Python

  •

  MIT License

  •0•1•0•0•Updated Nov 13, 2024Nov 13, 2024

• phg-docs

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

• Field-Book

  Public
  Field Book

  Java

  •

  GNU General Public License v2.0

  •58•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

  pythondockerbioinformatics+ 7rjupytergenomicsjupyter-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

  •24•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

  •81•0•0•0•Updated Jul 16, 2020Jul 16, 2020

• bwa-mem2

  Public
  The next version of bwa-mem

  C++

  •

  Other

  •108•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