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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 Nov 22, 2024Nov 22, 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•23•5•0•Updated Mar 19, 2023Mar 19, 2023

    • expvip-web

      Public
      expVIP. EXPression and VIsualisation Platform
      Ruby
      •
      MIT License
      •9•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•5•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 includ…
      Python
      •1•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•11•3•1•Updated May 10, 2021May 10, 2021

    • igv.js

      Public
      Embeddable genomic visualization component based on the Integrative Genomics Viewer
      JavaScript
      •
      MIT License
      •244•0•0•0•Updated May 6, 2021May 6, 2021

    • pangenome-haplotypes

      Public
      Scripts to do haplotype analysis on pan genomes.
      HTML
      •
      MIT License
      •2•20•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
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