Code and scripts for research papers

📃 A repository of repositories containing code and scripts used in research articles, papers and preprints

View as a web page or Github repository.

2026

Effects of different concentrations and combinations of antibiotics on the dynamics of intracellular transposition in Escherichia coli

Richard N. Goodman, Ellinor Shore, Michael S. M. Brouwer, Peter Nambala, Nicholas Feasey, Nina Langeland, Sabrina J. Moyo, Andrew Singer, Adam P. Roberts bioRxiv (preprint) ; doi: https://doi.org/10.64898/2026.07.24.740473

Repository of code for paper

• R script - Genomic visualisation of RS1 and RS2 (Figure 1)
• R script - Genomic visualisation of pBACpAK derivatives with Tn/IS inserts (Figure 4)
• R script - Analysing the effect of ceftrixone concentration on CFU/ml in RS1 and RS2 (Figure 2)
• R script - Correcting for clonal expansion
• R script - Transposition frequency analysis of PT, T and MT (Figure 3, Figure S3)
• R script - Variance (SEM) and difference (LFC) in PT, T and MT transpostion frequencies (Figure S2-3)
• R script - Insertion site analysis (Figure 5, Figure S4)

Shotgun metagenomic analysis of the oral microbiomes of children with noma

Michael Olaleye, Angus M O’Ferrall, Richard N. Goodman, Deogracia W Kabila, Miriam Peters, Gregoire Falq, Joseph Samuel, Donal Doyle, Diana Gomez, Gbemisola Oloruntuyi, Shafiu Isah, Adeniyi S Adetunji, Elise N. Farley, Nicholas J Evans, Mark Sherlock, Adam P. Roberts, Mohana Amirtharajah, Stuart Ainsworth PLOS Neglected Tropical Diseases 20(3): e0014118, https://doi.org/10.1101/2025.06.24.661267

Repository of code for paper

• Table 1A, Figures 1B, 2 and 3, Figures S2-S4 - Noma vs healthy dataset analysis
• Table 1B, Figure 1A, Figure S1 - Within Noma dataset analysis
• Within healthy dataset analysis

2025

Comparative genomics of blood and faecal E. coli and K. pneumoniae isolates from neonates with bloodstream infections in Tanzania

Richard N. Goodman, Sabrina J. Moyo, Ilinca Memelis, Aakash Khanijau, Joel Manyahi, Upendo O. Kibwana, Said Aboud, Bjørn Blomberg, Nina Langeland, Adam P. Roberts. Communications Biology 8, 1603 (2025), https://doi.org/10.1038/s42003-025-09008-5

Repository of code for paper

• Figure 1 - ANI and SNP distance matrices
• Figure 2 - core genome phylogenetic tree
• Figure 3 - variant calling heatmaps with breseq
• Figure 4 - circular whole genome comparisons
• Figure 5 - analysing virulence factor determinants

Genomic investigation of ESBL-producing Escherichia coli reveals likely transmission within and between One Health sectors in Jakarta, Indonesia

Nelly Puspandari, Rahadian Pratama, Richard N. Goodman, Imron Suandy, S Sunarno, Efadeswarni, Tati Febriana, Dwi Febriyana, S. Sunarno, Desrina Sitompul, Asih Hartanti, Ageng Wiyatno, Shannon Quek, Simon Wagstaff, Adam P. Roberts and Thomas R.D. Weaver Research Square (preprint)

Repository of code for paper

• Figure 2 - Geospatial distribution of STs across Jakarta
• Figure 4 - Geospatial mapping of waterways Jakarta Indonesia
• Figure 3A - ANI/SNP matrix for specific STs
• Figure 3B - Geospatial plotting ANI strain distance

2024

Molecular mechanisms of re-emerging chloramphenicol susceptibility in extended-spectrum beta-lactamase-producing Enterobacterales

Graf, F.E., Goodman, R.N., Gallichan, S. et al. Nature Communications 15, 9019 (2024). https://doi.org/10.1038/s41467-024-53391-2

Repository of code for paper

• Figure 4 - Co-occurence analysis of AMR genes