Dissecting the molecular mechanisms controlling crop heterosis using deep learning could accelerate crop improvement

This repository contains an R script for generating Circos plots to visualize accessory gene presence-absence patterns and expression levels in *Streptococcus pneumoniae* serotype 3. It compares clade I (PT8465) and clade II (ND6401) strains, highlighting differences in gene expression and adaptation.

A sophisticated bioinformatics pipeline for bacterial pangenome analysis, integrating WGS and RNA-Seq data. It enhances genome completeness with hybrid assemblies, identifies core/accessory genes, and enables pangenome-level transcriptomic profiling. Built on Snakemake, it is scalable, customizable, and optimized for strain-specific insights.