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adegenet: a R package for the multivariate analysis of genetic markers
Helper Functions for Interactive Tree Of Life (iTOL)
MaAsLin2: Microbiome Multivariate Association with Linear Models
Generating iToL annotations from Spreadsheet or CSV files
treeWAS: A Phylogenetic Tree-Based Tool for Genome-Wide Association Studies in Microbes
Bayesian inference of ancestral dates on bacterial phylogenetic trees
A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
post processing of bacterial pangenome gene presence/absence matrices
PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
AutoScore: An Interpretable Machine Learning-Based Automatic Clinical Score Generator
A pipeline for performing genome-wide association tests for bacterial genomes.
An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
Three bacterial GWAS methods all rolled into one easy-to-use R package
Infer transmission clusters from SNP and timing data
Nucmer from Mummer3 followed by ggplot for nicer and more customisable genome alignment plots.
Visualisation application for Klebsiella genotypes generated by Kleborate.
This is the code repository for reproducing analyses in the paper: CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids
regentrans: R package for investigating regional pathogen transmission using genomic data
SCORE - a consensus tool for detecting differentially expressed genes in bacteria
R package to perform data pre-processing for more informative bacterial GWAS
CNV detection for prokaryote genomes using NGS sequencing data
Repository to Hold Code base for 'The Intra-Host Evolutionary Landscape And Pathoadaptation Of Persistent Staphylococcus aureus In Chronic Rhinosinusitis' Paper
Active surveillance of newly-admitted nursing home patients for colonization of antibiotic-resistant bacteria reveals that multiple lineages have spread across southeast Michigan healthcare networks.
All scripts and results used in the K. pneumoniae paper