Shing Hei Zhan's repositories
3diphy
Maximum likelihood structural phylogenetics by including Foldseek 3Di characters. Supporting Information for Puente-Lelievre et al. 2023n for
angiosperm-chromosome-number-evolution
Analysis of the rates of chromosome number evolution and lineage diversification in major angiosperm clades.
lshmm
code to run Li and Stephens
onekg_analysis
Evaluation of genotype imputation methods using the unified genealogy dataset
sc2ts
Infer a succinct tree sequence from SARS-COV-2 variation data
tskit
Population-scale genomics
AllTheBacteria
Follow up to Grace Blackwell's 661k dataset, for 2023
atb_analysis
Anaysis of the bacterial genomes in AllTheBacteria
BDMM-Prime
Modified implementation of the BDMM multi-type birth-death model for BEAST 2.
CherryML
Scalable Maximum Likelihood Estimation of Phylogenetic Models
GRAPL
GRAPL: A computational library for nonparametric structural causal modelling, analysis and inference
hmmlearn
Hidden Markov Models in Python, with scikit-learn like API
numpy-100
100 numpy exercises (with solutions)
popgen-notes
Population genetics notes
Probabilistic-Programming-and-Bayesian-Methods-for-Hackers
aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)
pvae
code for "Continuous Hierarchical Representations with Poincaré Variational Auto-Encoders".
revbayes
Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
rustlings
:crab: Small exercises to get you used to reading and writing Rust code!
SINGER
Sampling and inference of genealogies with recombination
stat_rethinking_2023
Statistical Rethinking Course for Jan-Mar 2023
tb_genome_analysis
Analysis of whole genome sequences of M. tuberculosis
ts-mcmc
A simple prototype for using tskit to store phylogenetic MCMC output.
tskit_arg_visualizer
Interactive visualization method for ancestral recombination graphs
tsqc
Utilities for evaluating inferred tree sequences