johnlees

Research Group Leader at EMBL-EBI. Software is for statistical genetics/bacteria/genomic epidemiology/modelling

EMBL-EBICambridge, UK

Pinned Repositories

mandrake
Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding
Language:Python38 5 232
PopPUNK
PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
Language:Python100 6 23319
pp-sketchlib
Library of sketching functions used by PopPUNK
Language:C++30 3 538
ska.rust
Split k-mer analysis – version 2
Language:Rust96 6 477
unitig-caller
Methods to determine sequence element (unitig) presence/absence
Language:C++20 2 273
23andme-impute
Scripts and advice to run IMPUTE2 on 23 and me raw data
Language:Perl22 3 23
bioinformatics
Utilities written for bioinformatics
Language:Perl17 2 26
seer
sequence element (kmer) enrichment analysis
Language:C++45 6 7710
which_tree
Testing of phylogenetic inference methods
Language:R9 2 03
pyseer
SEER, reimplemented in python 🐍🔮
Language:Python125 9 23427

johnlees's Repositories

johnlees/seer
sequence element (kmer) enrichment analysis
Language:C++45 6 7710
johnlees/bioinformatics
Utilities written for bioinformatics
Language:Perl17 2 26
johnlees/rapidnj
Code for rapidNJ by Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen.
Language:C++3 1 01
johnlees/rapidNJ-M1
Fast implementation of the Neighbour-Joining method for phylogenetic inference (for M1 macs)
Language:C3 1 02
johnlees/glmnet_python
Language:Jupyter Notebook2 2 03
johnlees/PopPUNK-web
Web version of PopPUNK
Language:JavaScript2 2 15
johnlees/cuda_rng_benchmarking
Benchmarking the RNG in dust against curand
Language:Cuda1 1 0
johnlees/genometrackr_access
Downloading data from NCBI Genometrackr
Language:Python1 2 0
johnlees/one_hundred_lines
Activity for 100 lines of code
Language:R0 1 00
johnlees/advent-of-code-2021
Rust this time
Language:Rust2 0
johnlees/advent-of-code-2023
Advent of Code 2023 (rust again)
Language:Rust1 0
johnlees/advent-of-cuda
Trying to use brute force and parallelisation
Language:Cuda1 1
johnlees/BactDating
Bayesian inference of ancestral dates on bacterial phylogenetic trees
Language:R1 0
johnlees/carriage-age-plots
Code for plots in 'Pneumococcal genetic variability influences age-dependent bacterial carriage'
Language:R1 0
johnlees/cbl_test
Language:Rust1 0
johnlees/cmdstanr
CmdStanR: the R interface to CmdStan
Language:R1 0
johnlees/cpython
The Python programming language
Language:Python1 0
johnlees/genome-sketching
online notebooks for a review of genome sketching
Language:Jupyter Notebook1 0
johnlees/glmnet_py-feedstock
A conda-smithy repository for glmnet_py.
Language:Shell1 0
johnlees/hdbscan-debug
A high performance implementation of HDBSCAN clustering.
Language:Jupyter Notebook0 0
johnlees/hdbscan-feedstock
A conda-smithy repository for hdbscan.
0 0
johnlees/mandrake-feedstock
A conda-smithy repository for mandrake.
0 0
johnlees/MIC_prediction
Language:R0 0
johnlees/ntHash
ntHash: recursive nucleotide hashing
Language:C++0 0
johnlees/nvcc-feedstock
A conda-smithy repository for nvcc.
Language:Shell1 0
johnlees/odin-dust-plots
Code to recreate plots in 'Reproducible parallel inference and simulation of stochastic state space models using odin, dust, and mcstate'
Language:HTML1 0
johnlees/pneumo_core
Scripts to get some population genetics stats about core genes of S. pneumoniae
Language:Perl2 0
johnlees/pp-sketchlib-feedstock
A conda-smithy repository for pp-sketchlib.
1 0
johnlees/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
Language:Python2 0
johnlees/transmission_blp
Code for plots and simulations related to loss of diversity in S. pnuemoniae
Language:R1 0