AppliedBioinformatics

runBNG

An easy way to run BioNano genomic analysis

Brassica_oleracea_rapa_napus_code

Code for the Brassica oleracea/rapa/napus genomic comparison

BioNanoAnalyst

BioNanoAnalyst is a tool providing GUI to assess the genome assembly quality using BioNano data.

B_oleracea_R_genes_supplementary

This repository contains scripts used to generate the plots and results of the B. oleracea R-genes paper

pan_genome_scripts

Python scripts for constructing pangenomes using the iterative mapping style for the Bioinformatics Methods chapter: Making a Pan genome using the iterative mapping approach

gene-daisychain

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.

RefKA

A fast and efficient long-read genome assembly approach for large and complex genomes

pangenome

Python scripts designed to perform tasks associated with the pangenome construction method of iterative mapping and assembly

DiffKAP

A Differential k-mer Analysis Pipeline

PAV_table_scripts

Python scripts for constructing PAV tables for the Bioinformatics Methods chapter: Creating a Gene Presence/Absence Table using Mosdepth.

Basics-of-Bash

lncRNA_Prediction_Interpretation

Notebooks, Data and Scripts for lncRNA Prediction & Interpretation

maize_early_yield_prediction

Repository with the code for predicting the yield of crop varieties using deep learning and early phenotype data.

BioNanoScripts

Scripts used for BioNano analysis

H_ovalis_supplementary

legume_gene_count

Truegene