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    28 repositories

    • ShiuLab.github.io

      Public
      Shiu Lab Website
      JavaScript
      •
      MIT License
      •1•0•0•0•Updated May 27, 2026May 27, 2026

    • Manuscript_Code

      Public
      Repository for code used for publications
      Python
      •
      GNU General Public License v3.0
      •10•30•2•1•Updated Apr 23, 2026Apr 23, 2026

    • plant_sci_hist

      Public
      For dissecting major conceptual shifts in plant science
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 15, 2025Oct 15, 2025

    • ML_workshop

      Public
      Machine learning workshop materials
      Jupyter Notebook
      •
      MIT License
      •5•16•1•0•Updated Nov 19, 2024Nov 19, 2024

    • 2024_Ath_GP

      Public
      Python
      •
      GNU General Public License v3.0
      •5•13•0•0•Updated Oct 15, 2024Oct 15, 2024

    • ML-Pipeline

      Public
      A Semi-Automated Machine Learning Pipeline. Developed by the Shiu Lab. Implemented using SciKit-Learn
      Python
      •
      MIT License
      •15•28•3•0•Updated May 7, 2024May 7, 2024

    • pickle-corpus-code

      Public
      Code for the manuscript "In a PICKLE: Entity and relation annotation guidelines for the molecular plant sciences"
      Jupyter Notebook
      •2•1•0•0•Updated Dec 20, 2023Dec 20, 2023

    • plantbert

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 28, 2023Nov 28, 2023

    • plant_image_classify

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Nov 9, 2023Nov 9, 2023

    • PseudogenePipeline

      Public
      Python
      •
      Creative Commons Zero v1.0 Universal
      •20•41•10•0•Updated Jun 8, 2023Jun 8, 2023

    • GO-term-enrichment

      Public
      Python
      •3•4•0•0•Updated Feb 3, 2023Feb 3, 2023

    • Utilities

      Public
      Scripts useful for manipulation and basic analysis of common file types
      Python
      •1•3•0•0•Updated May 25, 2022May 25, 2022

    • MotifDiscovery

      Public
      Working with RandomForest in python and R to improve motif discovery
      Python
      •2•2•0•0•Updated Oct 13, 2021Oct 13, 2021

    • Switchgrass_genome_prediction

      Public
      0•0•0•0•Updated Jul 7, 2021Jul 7, 2021

    • RNA-seq_data_processing

      Public
      Python
      •
      MIT License
      •4•0•0•0•Updated Jun 19, 2021Jun 19, 2021

    • Pathway_gene_prediction_in_tomato

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Apr 2, 2021Apr 2, 2021

    • ml-reading-group

      Public
      Using yeast DM fitness data to try out methods from ML reading group
      Jupyter Notebook
      •1•0•0•0•Updated Aug 25, 2020Aug 25, 2020

    • MotifDiscovery-legacy-

      Public
      Lab scripts to find and analyze pCREs.
      Tcl
      •1•1•0•0•Updated Aug 14, 2020Aug 14, 2020

    • RNAseq_pipeline

      Public
      Python
      •
      MIT License
      •7•6•0•0•Updated Jul 22, 2020Jul 22, 2020

    • Gene_coexpression_scripts

      Public
      R
      •3•4•0•0•Updated Feb 20, 2020Feb 20, 2020

    • Evaluating-misassembly

      Public
      Factors influencing and machine learning models predicting read coverage in a genome assembled using short reads
      Python
      •2•2•0•0•Updated Jan 13, 2020Jan 13, 2020

    • SM-gene_prediction_Slycopersicum

      Public
      This repository will have all scripts and/or links to pipelines used for the SM gene prediction in S. lycopersicum paper
      Python
      •3•1•1•0•Updated Apr 28, 2019Apr 28, 2019

    • Tree_building

      Public
      Use for getting orthologs, building trees, or reconciling trees
      Python
      •1•0•0•0•Updated Feb 28, 2019Feb 28, 2019

    • ANN_Pipeline

      Public
      Shiu Lab code base for Artificial Neural Networks implemented in Tensorflow
      Python
      •1•0•0•0•Updated Feb 22, 2019Feb 22, 2019

    • GenomicSelection

      Public
      R
      •4•4•0•0•Updated Dec 11, 2018Dec 11, 2018

    • CRE-Pipeline

      Public
      pCRE pipeline
      Python
      •0•0•0•0•Updated Aug 30, 2017Aug 30, 2017

    • GenomeMatrixProcessing

      Public
      Python
      •0•0•0•0•Updated Apr 14, 2017Apr 14, 2017

    • Weka-Grid-Search

      Public
      Scripts needed to run weka
      Python
      •0•0•0•0•Updated Jun 10, 2016Jun 10, 2016
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