Repositories list

• TRG-ImageProcessing

  Public
  Swarts Lab CNN stuff

  Python

  •

  MIT License

  •55 forks•1414 stars•22 issues•11 pull request•Updated Jun 18, 2026Jun 18, 2026

• kok_2025

  Public
  Code for paper

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 13, 2026Feb 13, 2026

• bookend

  Public
  End-guided RNA assembler

  Python

  •

  MIT License

  •11 fork•1515 stars•22 issues•00 pull requests•Updated Dec 2, 2025Dec 2, 2025

• mplight

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 6, 2025Nov 6, 2025

• vikas_states_tf_study_2025

  Public
  Nextflow

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 23, 2025Jul 23, 2025

• 1001Gplus_paper

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•33 stars•00 issues•00 pull requests•Updated Jul 2, 2025Jul 2, 2025

• aradeepopsis

  Public
  A versatile, fully open-source pipeline to extract phenotypic measurements from plant images

  deep-learningnextflowtensorflow+ 4

  deep-learningnextflowtensorflowscikit-imagesemantic-segmentationplant-phenotypingarabidopsis-thaliana

  Nextflow

  •

  GNU General Public License v3.0

  •1010 forks•5252 stars•22 issues•11 pull request•Updated May 26, 2025May 26, 2025

• PROalign

  Public
  Modified from https://github.com/JAJ256/PROseq_alignment.sh

  Shell

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 21, 2024May 21, 2024

• nf-haplocaller

  Public
  Nextflow pipeline for GATK best practices (HaplotypeCaller)

  Nextflow

  •

  MIT License

  •22 forks•00 stars•11 issue•00 pull requests•Updated Mar 8, 2024Mar 8, 2024

• GWA-Portal

  Public
  Web-app to store an display GWAS studies

  Java

  •55 forks•55 stars•6161 issues•77 pull requests•Updated Feb 29, 2024Feb 29, 2024

• nanoPARE

  Public
  RNA 5' analysis tools for use with the nanoPARE protocol

  Python

  •

  GNU General Public License v3.0

  •11 fork•22 stars•55 issues•00 pull requests•Updated Feb 8, 2024Feb 8, 2024

• SNPmatch

  Public
  A simple python library to identify the most likely strain from the population

  snpspipelinegenotype+ 6

  snpspipelinegenotypegenotyping-by-sequencingarabidopsisgenotypingsnpmatcharageno1001genomes

  Python

  •

  MIT License

  •55 forks•1010 stars•22 issues•00 pull requests•Updated Jan 11, 2024Jan 11, 2024

• gwas_workshop

  Public
  basic GWAS workshop in jupyter notebook form

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •33 forks•00 stars•00 issues•00 pull requests•Updated Oct 2, 2023Oct 2, 2023

• jamge_states_2023

  Public
  Code and data for figures in elife paper

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 9, 2023May 9, 2023

• gwaR

  Public
  A collection of R functions to conduct downstream GWAS analysis for arabidopsis thaliana.

  gwasrarabidopsis-thaliana

  gwasrarabidopsis-thaliana

  R

  •

  MIT License

  •11 fork•55 stars•00 issues•00 pull requests•Updated Jan 30, 2023Jan 30, 2023

• PhenoBox-System

  Public
  The “Phenobox”, a flexible, automated, open-source plant phenotyping solution

  Python

  •

  GNU General Public License v2.0

  •55 forks•55 stars•00 issues•1616 pull requests•Updated Dec 7, 2022Dec 7, 2022

• pisupati-gbm-paper-2022

  Public
  Supplementary data and notebooks required for the paper.

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 3, 2022Dec 3, 2022

• RNASeqWebApp

  Public
  Python

  •00 forks•00 stars•00 issues•55 pull requests•Updated Jun 22, 2022Jun 22, 2022

• GWAPP

  Public
  HTML

  •00 forks•11 star•00 issues•44 pull requests•Updated Jun 22, 2022Jun 22, 2022

• singularity-jupyterlab-sos

  Public
  Jupyterlab container with SOS kernels

  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 22, 2022May 22, 2022

• pyBsHap

  Public
  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated May 19, 2022May 19, 2022

• gwaportal-hpc-pipeline

  Public
  HPC pipeline for GWA-Portal

  Python

  •

  BSD 2-Clause "Simplified" License

  •00 forks•00 stars•00 issues•11 pull request•Updated Jan 6, 2022Jan 6, 2022

• RKP2021-CMT3

  Public
  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 23, 2021Apr 23, 2021

• GWAS-nf

  Public archive
  Nextflow pipeline to run genome wide association studies using limix

  Nextflow

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Apr 22, 2021Apr 22, 2021

• ScanPlateSeg

  Public
  Python scripts for detection and alignment of dish in scanned seedling data

  Python

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 25, 2021Mar 25, 2021

• test-data

  Public
  Repository that stores test datasets for CI testing

  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 16, 2021Feb 16, 2021

• dormancy

  Public
  Dormancy Paper infos

  R

  •11 fork•22 stars•00 issues•00 pull requests•Updated Jan 18, 2021Jan 18, 2021

• riboflow

  Public
  Pipeline for Ribosome Profiling Data

  Groovy

  •

  MIT License

  •88 forks•00 stars•00 issues•00 pull requests•Updated Jan 4, 2021Jan 4, 2021

• easybuild-easyconfigs

  Public
  A collection of easyconfig files that describe which software to build using which build options with EasyBuild.

  Python

  •

  GNU General Public License v2.0

  •785785 forks•00 stars•00 issues•00 pull requests•Updated Oct 16, 2020Oct 16, 2020

• gwaportal-gwas-server

  Public
  Server for accessing HDF5 files and python analysis from GWA-Portal

  Python

  •

  MIT License

  •00 forks•00 stars•22 issues•00 pull requests•Updated Jul 21, 2020Jul 21, 2020