John Lees's Projects
Scripts and advice to run IMPUTE2 on 23 and me raw data
Rust this time
Advent of Code 2023 (rust again)
Trying to use brute force and parallelisation
Apegrunt is a library that implements a space-efficient deduplicated data structure for storing and handling aligned sets of categorical data.
Bayesian inference of ancestral dates on bacterial phylogenetic trees
Utilities written for bioinformatics
Code for plots in 'Pneumococcal genetic variability influences age-dependent bacterial carriage'
Code for pneumococcal carriage duration
CmdStanR: the R interface to CmdStan
Resident vs challenger competition model for S. pneumoniae
Config files stored in ~
The Python programming language
Benchmarking the RNG in dust against curand
Distributed String Mining Framework
scripts and methods for fast bacterial genomic epidemiology
pairwise bacterial/human variant association
light version of dsm
online notebooks for a review of genome sketching
Downloading data from NCBI Genometrackr
A conda-smithy repository for glmnet_py.
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
A high performance implementation of HDBSCAN clustering.
A conda-smithy repository for hdbscan.
A conda-smithy repository for mandrake.
Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index