Repositories list

• 2024_Ath_GP

  Public
  Python

  •

  GNU General Public License v3.0

  •3•5•0•0•Updated Oct 15, 2024Oct 15, 2024

• ShiuLab.github.io

  Public
  Shiu Lab Website

  JavaScript

  •

  MIT License

  •1•0•0•0•Updated Aug 22, 2024Aug 22, 2024

• plant_sci_hist

  Public
  For dissecting major conceptual shifts in plant science

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jul 22, 2024Jul 22, 2024

• Manuscript_Code

  Public
  Repository for code used for publications

  Python

  •

  GNU General Public License v3.0

  •10•26•2•1•Updated Jun 29, 2024Jun 29, 2024

• ML_workshop

  Public
  Machine learning workshop materials

  Jupyter Notebook

  •

  MIT License

  •4•14•1•0•Updated May 16, 2024May 16, 2024

• ML-Pipeline

  Public
  A Semi-Automated Machine Learning Pipeline. Developed by the Shiu Lab. Implemented using SciKit-Learn

  Python

  •

  MIT License

  •13•24•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•0•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•0•0•0•Updated Nov 9, 2023Nov 9, 2023

• PseudogenePipeline

  Public
  Python

  •

  Creative Commons Zero v1.0 Universal

  •18•36•8•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•1•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•2•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