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    68 repositories

    • TRG-ImageProcessing

      Public
      Swarts Lab CNN stuff
      Python
      •
      MIT License
      •5•12•2•1•Updated Oct 28, 2025Oct 28, 2025

    • bookend

      Public
      End-guided RNA assembler
      Python
      •
      MIT License
      •1•15•2•0•Updated Aug 19, 2025Aug 19, 2025

    • vikas_states_tf_study_2025

      Public
      Nextflow
      •0•0•0•0•Updated Jul 23, 2025Jul 23, 2025

    • 1001Gplus_paper

      Public
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jul 2, 2025Jul 2, 2025

    • aradeepopsis

      Public
      A versatile, fully open-source pipeline to extract phenotypic measurements from plant images
      deep-learningnextflowtensorflowscikit-imagesemantic-segmentationplant-phenotypingarabidopsis-thaliana
      Nextflow
      •
      GNU General Public License v3.0
      •8•45•2•1•Updated May 26, 2025May 26, 2025

    • PROalign

      Public
      Modified from https://github.com/JAJ256/PROseq_alignment.sh
      Shell
      •
      MIT License
      •1•0•0•0•Updated May 21, 2024May 21, 2024

    • nf-haplocaller

      Public
      Nextflow pipeline for GATK best practices (HaplotypeCaller)
      Nextflow
      •
      MIT License
      •2•0•1•0•Updated Mar 8, 2024Mar 8, 2024

    • GWA-Portal

      Public
      Web-app to store an display GWAS studies
      Java
      •5•5•61•7•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
      •2•1•5•0•Updated Feb 8, 2024Feb 8, 2024

    • SNPmatch

      Public
      A simple python library to identify the most likely strain from the population
      snpspipelinegenotypegenotyping-by-sequencingarabidopsisgenotypingsnpmatcharageno1001genomes
      Python
      •
      MIT License
      •5•9•2•0•Updated Jan 11, 2024Jan 11, 2024

    • gwas_workshop

      Public
      basic GWAS workshop in jupyter notebook form
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Oct 2, 2023Oct 2, 2023

    • jamge_states_2023

      Public
      Code and data for figures in elife paper
      R
      •0•0•0•0•Updated May 9, 2023May 9, 2023

    • gwaR

      Public
      A collection of R functions to conduct downstream GWAS analysis for arabidopsis thaliana.
      gwasrarabidopsis-thaliana
      R
      •
      MIT License
      •1•5•0•0•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
      •5•5•0•16•Updated Dec 7, 2022Dec 7, 2022

    • pisupati-gbm-paper-2022

      Public
      Supplementary data and notebooks required for the paper.
      Jupyter Notebook
      •0•0•0•0•Updated Dec 3, 2022Dec 3, 2022

    • RNASeqWebApp

      Public
      Python
      •0•0•0•5•Updated Jun 22, 2022Jun 22, 2022

    • GWAPP

      Public
      HTML
      •0•1•0•4•Updated Jun 22, 2022Jun 22, 2022

    • singularity-jupyterlab-sos

      Public
      Jupyterlab container with SOS kernels
      Shell
      •0•0•0•0•Updated May 22, 2022May 22, 2022

    • pyBsHap

      Public
      Python
      •0•1•0•0•Updated May 19, 2022May 19, 2022

    • gwaportal-hpc-pipeline

      Public
      HPC pipeline for GWA-Portal
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•1•Updated Jan 6, 2022Jan 6, 2022

    • RKP2021-CMT3

      Public
      R
      •1•0•0•0•Updated Apr 23, 2021Apr 23, 2021

    • GWAS-nf

      Public archive
      Nextflow pipeline to run genome wide association studies using limix
      Nextflow
      •
      MIT License
      •2•0•0•0•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
      •0•1•0•0•Updated Mar 25, 2021Mar 25, 2021

    • test-data

      Public
      Repository that stores test datasets for CI testing
      0•0•0•0•Updated Feb 16, 2021Feb 16, 2021

    • dormancy

      Public
      Dormancy Paper infos
      R
      •1•2•0•0•Updated Jan 18, 2021Jan 18, 2021

    • riboflow

      Public
      Pipeline for Ribosome Profiling Data
      Groovy
      •
      MIT License
      •10•0•0•0•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
      •760•0•0•0•Updated Oct 16, 2020Oct 16, 2020

    • gwaportal-gwas-server

      Public
      Server for accessing HDF5 files and python analysis from GWA-Portal
      Python
      •
      MIT License
      •0•0•2•0•Updated Jul 21, 2020Jul 21, 2020

    • nf-methylpy

      Public
      Nextflow pipeline for running methylpy
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated May 12, 2020May 12, 2020

    • image-jenkins

      Public
      Jenkins CasC container image
      Groovy
      •0•0•0•0•Updated Jan 25, 2020Jan 25, 2020