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@AppliedBioinformatics AppliedBioinformatics

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    Repositories list

    18 repositories

    • biomarkit

      Public
      A publisher agnostic framework for downloading and converting full-text scientific publications to standardised markdown format.
      Python
      •0•0•0•0•Updated Aug 12, 2026Aug 12, 2026

    • legume_gene_count

      Public
      R
      •0•0•0•0•Updated Jun 17, 2022Jun 17, 2022

    • Truegene

      Public
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated May 2, 2022May 2, 2022

    • lncRNA_Prediction_Interpretation

      Public
      Notebooks, Data and Scripts for lncRNA Prediction & Interpretation
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Feb 19, 2022Feb 19, 2022

    • gene-daisychain

      Public
      A web server linking genome annotations. Aimed at researchers working on single genes that want to know what the homolog in other published assemblies is.
      JavaScript
      •
      GNU Lesser General Public License v3.0
      •2•3•0•0•Updated Dec 17, 2021Dec 17, 2021

    • maize_early_yield_prediction

      Public
      Repository with the code for predicting the yield of crop varieties using deep learning and early phenotype data.
      MIT License
      •3•0•0•0•Updated Jul 22, 2021Jul 22, 2021

    • Brassica_oleracea_rapa_napus_code

      Public
      Code for the Brassica oleracea/rapa/napus genomic comparison
      Jupyter Notebook
      •
      MIT License
      •5•16•0•0•Updated Apr 29, 2021Apr 29, 2021

    • runBNG

      Public
      An easy way to run BioNano genomic analysis
      Shell
      •
      MIT License
      •6•27•12•0•Updated Apr 9, 2021Apr 9, 2021

    • PAV_table_scripts

      Public
      Python scripts for constructing PAV tables for the Bioinformatics Methods chapter: Creating a Gene Presence/Absence Table using Mosdepth.
      Python
      •0•1•1•0•Updated Feb 23, 2021Feb 23, 2021

    • Basics-of-Bash

      Public
      1•0•0•0•Updated Jan 28, 2021Jan 28, 2021

    • pangenome

      Public
      Python scripts designed to perform tasks associated with the pangenome construction method of iterative mapping and assembly
      Python
      •
      MIT License
      •0•2•1•0•Updated Dec 7, 2020Dec 7, 2020

    • BioNanoAnalyst

      Public
      BioNanoAnalyst is a tool providing GUI to assess the genome assembly quality using BioNano data.
      Python
      •
      GNU General Public License v3.0
      •8•12•10•1•Updated Oct 30, 2020Oct 30, 2020

    • pan_genome_scripts

      Public
      Python scripts for constructing pangenomes using the iterative mapping style for the Bioinformatics Methods chapter: Making a Pan genome using the iterative map…
      Python
      •2•4•0•0•Updated Jul 30, 2020Jul 30, 2020

    • RefKA

      Public
      A fast and efficient long-read genome assembly approach for large and complex genomes
      Python
      •1•3•0•0•Updated Apr 19, 2020Apr 19, 2020

    • B_oleracea_R_genes_supplementary

      Public
      This repository contains scripts used to generate the plots and results of the B. oleracea R-genes paper
      R
      •
      MIT License
      •2•7•0•0•Updated Sep 21, 2018Sep 21, 2018

    • H_ovalis_supplementary

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 26, 2018Jul 26, 2018

    • DiffKAP

      Public
      A Differential k-mer Analysis Pipeline
      Perl
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated Aug 14, 2017Aug 14, 2017

    • BioNanoScripts

      Public
      Scripts used for BioNano analysis
      Python
      •
      MIT License
      •1•0•0•0•Updated Jun 29, 2017Jun 29, 2017
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