nickjcroucher

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

multilocusNFDS

pneumo-cgmlst

Core genome COGs for S. pneumoniae from Corander et al 2017 Nat. Ecol. Evol. 1:1950-60

progressionEstimation

R package for the estimation of microbial progression rates

bioconda-recipes

Conda recipes for the bioconda channel.

elfi

ELFI - Engine for Likelihood-Free Inference

genoPlotR

:exclamation: This is a read-only mirror of the CRAN R package repository. genoPlotR — Plot Publication-Grade Gene and Genome Maps. Homepage: http://genoplotr.r-forge.r-project.org/

maelaAntigens

R markdown document, and associated code, used for the analysis of the IgG immune response to pneumococcal proteins

mgeTransformation

Model of horizontal DNA transfer within a simple bacterial community

pbp_AMR_prediction

Research code for a project aimed at improving our understanding of the genetic determinants of antibiotic resistance in Streptococcus pneumoniae

pbp_tpd_extraction

pp-sketchlib

Library of sketching functions used by PopPUNK

PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

RCandy

RCandy: an R package for visualising homologous recombination events in bacterial genomes

recognise

Precise inference of bacterial recombinations

ska.rust

Split k-mer analysis – version 2

transposonDynamics