https://github.com/johnlees/seer

sequence element (kmer) enrichment analysis

bacteria gwas k-mer

Last synced: 14 Aug 2025

https://github.com/johnlees/23andme-impute

Scripts and advice to run IMPUTE2 on 23 and me raw data

Last synced: 14 Aug 2025

https://github.com/johnlees/which_tree

Testing of phylogenetic inference methods

Last synced: 14 Aug 2025

https://github.com/johnlees/tajima-d

calculates tajima's D from bcftools query input

Last synced: 14 Aug 2025

https://github.com/johnlees/efficient-bge

scripts and methods for fast bacterial genomic epidemiology

Last synced: 14 Aug 2025

https://github.com/johnlees/poppunk-web

Web version of PopPUNK

epidemiology frontend poppunk sketching

Last synced: 14 Aug 2025

https://github.com/johnlees/genometrackr_access

Downloading data from NCBI Genometrackr

Last synced: 14 Aug 2025

https://github.com/johnlees/paired-samples

Scripts and plots used for 'Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis'

Last synced: 14 Aug 2025

https://github.com/johnlees/rapidnj

Code for rapidNJ by Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen.

Last synced: 27 Oct 2025

https://github.com/johnlees/meningene

Programs and scripts used for analysis of the meningene cohort

Last synced: 14 Aug 2025

https://github.com/johnlees/pyseer

SEER, reimplemented in python

Last synced: 14 Aug 2025

https://github.com/johnlees/cuda_rng_benchmarking

Benchmarking the RNG in dust against curand

Last synced: 14 Aug 2025

https://github.com/johnlees/advent-of-code-2023

Advent of Code 2023 (rust again)

Last synced: 14 Aug 2025

https://github.com/johnlees/epistasis-code

pairwise bacterial/human variant association

Last synced: 14 Aug 2025

https://github.com/johnlees/pneumo_core

Scripts to get some population genetics stats about core genes of S. pneumoniae

Last synced: 14 Aug 2025

https://github.com/johnlees/advent-of-code-2021

Rust this time

Last synced: 14 Aug 2025

https://github.com/johnlees/pmcmc

Parallel implementation of MCMC using MPI - coded by Hákon Jónsson, John Lees and Tobias Madsen

Last synced: 14 Aug 2025

https://github.com/johnlees/carriage-age-plots

Code for plots in 'Pneumococcal genetic variability influences age-dependent bacterial carriage'

Last synced: 10 Sep 2025

https://github.com/johnlees/poppunk_galaxy

Galaxy tool for PopPUNK

Last synced: 08 Feb 2026

https://github.com/johnlees/poppunk-scripts

Scripts used to help produce extra analysis for the PopPUNK manuscript

Last synced: 24 Aug 2025

https://github.com/johnlees/odin-dust-plots

Code to recreate plots in 'Reproducible parallel inference and simulation of stochastic state space models using odin, dust, and mcstate'

Last synced: 11 Feb 2026

https://github.com/johnlees/johnlees.github.io

Last synced: 10 Feb 2026

https://github.com/johnlees/cbl_test

Last synced: 20 Sep 2025

https://github.com/johnlees/transmission_blp

Code for plots and simulations related to loss of diversity in S. pnuemoniae

Last synced: 14 Aug 2025

https://github.com/johnlees/one_hundred_lines

Activity for 100 lines of code

Last synced: 14 Aug 2025

https://github.com/johnlees/config

Config files stored in ~

Last synced: 04 Oct 2025

https://github.com/johnlees/pilus-age

Association between pilus and age in the Maela dataset

Last synced: 14 Aug 2025

https://github.com/johnlees/derangement

Last synced: 14 Aug 2025

https://github.com/johnlees/r_plots

Some scripts to create plots in R

Last synced: 14 Aug 2025

https://github.com/johnlees/advent-of-cuda

Trying to use brute force and parallelisation

Last synced: 14 Aug 2025

https://github.com/johnlees/carriage-duration

Code for pneumococcal carriage duration

Last synced: 14 Aug 2025

https://github.com/johnlees/competition_model

Resident vs challenger competition model for S. pneumoniae

Last synced: 14 Aug 2025