Pinned Repositories
3diphy
Maximum likelihood structural phylogenetics by including Foldseek 3Di characters. Supporting Information for Puente-Lelievre et al. 2023n for
CSSR-R
R interface to CSSR program, authored by https://github.com/stites/CSSR
game-on
Analysis of League of Legends game data
lshmm
code to run Li and Stephens
pyHarmonySearch
pyHarmonySearch is a pure Python implementation of the harmony search (HS) global optimization algorithm.
pyrqa
Recurrence Quantification Analysis of Large-Scale Time Series
sc2ts
Infer a succinct tree sequence from SARS-COV-2 variation data
tsimpute
Genome-wide genotype imputation using tree sequences.
tskit
Population-scale genomics
szhan's Repositories
szhan/pyrqa
Recurrence Quantification Analysis of Large-Scale Time Series
szhan/3diphy
Maximum likelihood structural phylogenetics by including Foldseek 3Di characters. Supporting Information for Puente-Lelievre et al. 2023n for
szhan/lshmm
code to run Li and Stephens
szhan/onekg_analysis
Evaluation of genotype imputation methods using the unified genealogy dataset
szhan/sc2ts
Infer a succinct tree sequence from SARS-COV-2 variation data
szhan/sc2ts-paper
szhan/tsimpute
Genome-wide genotype imputation using tree sequences.
szhan/tskit
Population-scale genomics
szhan/AllTheBacteria
Follow up to Grace Blackwell's 661k dataset, for 2023
szhan/atb_analysis
Anaysis of the bacterial genomes in AllTheBacteria
szhan/BDMM-Prime
Modified implementation of the BDMM multi-type birth-death model for BEAST 2.
szhan/CherryML
Scalable Maximum Likelihood Estimation of Phylogenetic Models
szhan/giglib
szhan/GRAPL
GRAPL: A computational library for nonparametric structural causal modelling, analysis and inference
szhan/hmmlearn
Hidden Markov Models in Python, with scikit-learn like API
szhan/numpy-100
100 numpy exercises (with solutions)
szhan/popgen-notes
Population genetics notes
szhan/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 ;)
szhan/pvae
code for "Continuous Hierarchical Representations with Poincaré Variational Auto-Encoders".
szhan/revbayes
Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
szhan/rse-course
Materials for Turing's Research Software Engineering course
szhan/rustlings
:crab: Small exercises to get you used to reading and writing Rust code!
szhan/shing-course-repo
RSE
szhan/SINGER
Sampling and inference of genealogies with recombination
szhan/stat_rethinking_2023
Statistical Rethinking Course for Jan-Mar 2023
szhan/tb_genome_analysis
Analysis of whole genome sequences of M. tuberculosis
szhan/treeflow
szhan/ts-mcmc
A simple prototype for using tskit to store phylogenetic MCMC output.
szhan/tskit_arg_visualizer
Interactive visualization method for ancestral recombination graphs
szhan/tsqc
Utilities for evaluating inferred tree sequences