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    21 repositories

    • transcript_to_genomic_loci

      Public
      Translating transcript-relative loci to genome-relative loci
      R
      •1•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • tef_kGWAS_2024

      Public
      Custom bash and R code used for a project applying k-mer-based GWAS to a range of agronomic and grain metabolite traits in tef (Eragrostis tef)
      R
      •
      MIT License
      •1•0•0•0•Updated Sep 4, 2024Sep 4, 2024

    • Uauy_Lab_RNAseq_mapping_pipeline

      Public
      A small pipeline for generating transcriptomic data from raw FASTQ files via Fastp trimming and Kallisto pseudoalignment.
      Shell
      •
      MIT License
      •1•0•0•0•Updated Nov 22, 2023Nov 22, 2023

    • MLP_finding

      Public
      Python
      •0•0•0•0•Updated Sep 23, 2023Sep 23, 2023

    • IBSpy

      Public
      Python library to identify Identical By State regions
      C++
      •
      MIT License
      •4•14•3•0•Updated Mar 19, 2023Mar 19, 2023

    • expvip-web

      Public
      expVIP. EXPression and VIsualisation Platform
      Ruby
      •
      MIT License
      •10•17•14•6•Updated Mar 8, 2023Mar 8, 2023

    • pangenome-web

      Public
      Web visualisation of regions identical by descent.
      Ruby
      •0•6•5•24•Updated Jan 19, 2023Jan 19, 2023

    • pyensemblorthologues

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 11, 2022Oct 11, 2022

    • monococcum_introgressions

      Public
      Analysis of monococcum introgressions into hexaploid wheat
      Jupyter Notebook
      •3•2•0•0•Updated Sep 19, 2022Sep 19, 2022

    • ML-carpel_traits

      Public
      This repository contains the training codes for the development of the model used to quantify stigma area and ovary diameter. The trained models are also included. R scripts used for data organisation and visualisation are provided.
      Python
      •0•1•0•0•Updated Jul 4, 2022Jul 4, 2022

    • biojs-vis-expression-bar

      Public
      JavaScript
      •
      MIT License
      •5•2•8•0•Updated Dec 5, 2021Dec 5, 2021

    • bioruby-polymarker

      Public
      Webinterface for PolyMarker
      CSS
      •3•2•5•0•Updated Jun 14, 2021Jun 14, 2021

    • bioruby-polyploid-tools

      Public
      Library and tools to deal with polyploid genomics
      Ruby
      •11•10•3•0•Updated May 10, 2021May 10, 2021

    • igv.js

      Public
      Embeddable genomic visualization component based on the Integrative Genomics Viewer
      JavaScript
      •
      MIT License
      •230•0•0•0•Updated May 6, 2021May 6, 2021

    • pangenome-haplotypes

      Public
      Scripts to do haplotype analysis on pan genomes.
      HTML
      •
      MIT License
      •3•21•1•0•Updated Sep 24, 2020Sep 24, 2020

    • GENIE3_scripts

      Public
      Scripts used in the manuscript "Validation and characterisation of the wheat GENIE3 network using an independent RNA-Seq dataset." from Harrington et al. 2019
      R
      •3•1•0•0•Updated Jul 30, 2020Jul 30, 2020

    • bio.tilling

      Public
      R scripts to plot/analyse coverage from BED files
      R
      •2•0•0•0•Updated Jul 20, 2020Jul 20, 2020

    • bioruby-pangenome

      Public
      Scripts for the pan genome analysis
      Ruby
      •
      MIT License
      •0•8•0•0•Updated Jun 4, 2020Jun 4, 2020

    • WheatHomoeologExpression

      Public
      Jupyter Notebook
      •9•15•1•0•Updated May 31, 2020May 31, 2020

    • EMS-filter

      Public
      Notebooks on how to filter EMS mutations from noise
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 23, 2019Jul 23, 2019

    • K2282_scripts

      Public
      Scripts from the K2282 Mapping Paper
      Shell
      •2•0•0•0•Updated Apr 28, 2019Apr 28, 2019