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/game-on
Analysis of League of Legends game data
szhan/CSSR-R
R interface to CSSR program, authored by https://github.com/stites/CSSR
szhan/pyHarmonySearch
pyHarmonySearch is a pure Python implementation of the harmony search (HS) global optimization algorithm.
szhan/avocado_meets_ml
Yep, avocado meets machine learning.
szhan/bio_corex
A flexible version of CorEx developed for bio-data challenges that handles missing data, continuous/discrete variables, multi-CPU, overlapping structure, and includes visualizations
szhan/coco
Numerical Black-Box Optimization Benchmarking Framework
szhan/tsinfer
Infer a tree sequence from genetic variation data.
szhan/bdendro
Bokeh helpers for visualizing a dendrogram.
szhan/cpp-recipes
Source code for 'C++ Recipes' by Bruce Sutherland
szhan/ecdyn
szhan/esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
szhan/factorial_hmm
FactorialHMM, a Python package for fast exact inference in Factorial Hidden Markov Models
szhan/genomegaMap
Within-species genome-wide dN/dS estimation from very many genomes
szhan/imodels
Interpretable ML package 🔍 for concise, transparent, and accurate predictive modeling (sklearn-compatible).
szhan/inst-spec
R scripts and data files to test the "instant speciation" hypothesis
szhan/memory
Analysis for CSSS2017 "memory" team
szhan/nltk
NLTK Source
szhan/pagmo2
A C++ / Python platform to perform parallel computations of optimisation tasks (global and local) via the asynchronous generalized island model.
szhan/phylokit
Phylogenetics toolkit for the PyData Ecosystem
szhan/protein-sequence-models
szhan/pytisean
Tisean python wrapper
szhan/rhododb
Phylogenomic resource to study the community ecology of the red algae
szhan/szhan.github.io
Personal website
szhan/tsconvert
Utilities for converting tree sequences to and from other formats
szhan/tskit_tutorials
A set of tutorials for msprime and tskit.
szhan/unified_genealogy_paper
A Unified Genealogy of Modern and Ancient Humans
szhan/vbsky
Variational Bayesian skyline infers evolutionary models from large amounts of phylogenetic data.