bbeckley-hub/nigeria-saureus-biofilm-genomics

Genomic profiling of biofilm‑associated genes in clinical Staphylococcus aureus from Nigeria: association with multidrug resistance and clonal lineages # Supplementary Data for: Genomic profiling of biofilm‑associated genes in clinical *Staphylococcus aureus* from Nigeria This repository contains all supplementary data, analysis scripts, and results for the manuscript: **Genomic profiling of biofilm‑associated genes in clinical *Staphylococcus aureus* from Nigeria: association with multidrug resistance and clonal lineages** **Authors:** Brown Beckley, Christiana Jesumirhewe, Solomon Babajide Bamiro, Vincent Amarh, Abdurrahman Hassan Jibril, Innocent Afeke, Adesola Olalekan --- ## Repository Structure ``` . ├── Rscripts/ # All analysis scripts │ ├── analysis_*.R # R scripts for statistical analyses │ ├── build_biofilm_dataset_expanded.py # Python script to build dataset │ ├── convert_figures.sh # Convert figures to multiple formats │ ├── R_packages.txt # Required R packages │ └── run_all_analyses.sh # Master script to run all analyses │ ├── supplementary/ # Supplementary data and outputs │ ├── Supplementary files/ # Organised supplementary tables & figures │ │ ├── Supplementary Data/ # Raw StaphScope output files │ │ ├── Supplementary_Table_S*.csv # Supplementary tables (S1–S9) │ │ └── Supplementary_Figure_S*.pdf# Supplementary figures (S1–S3) │ │ │ ├── figures/ # Main manuscript figures (1–8) │ │ ├── Figure_1_*.pdf/png/tif │ │ ├── Figure_2_*.pdf/png/tif │ │ ├── ... │ │ └── Figure_8_*.pdf/png/tif │ │ │ └── extras/ # Intermediate files and additional outputs │ ├── amr_genes.csv │ ├── bacmet_genes.csv │ ├── biofilm_analysis_dataset_expanded.csv │ ├── sample_overview.csv │ └── virulence_genes.csv │ └── README.md # This file ``` --- ## Supplementary Tables (CSV) | Table | Description | |-------|-------------| | **S1** | Clinical metadata for all 1 …