Shing Hei Zhan (szhan)

szhan

Geek Repo

Company:University of Oxford

Location:Oxford, United Kingdom

Home Page:https://scholar.google.ca/citations?user=2nS6Z44AAAAJ&hl=en

Twitter:@shingheizhan

Github PK Tool:Github PK Tool


Organizations
tskit-dev

Shing Hei Zhan's repositories

pyrqa

Recurrence Quantification Analysis of Large-Scale Time Series

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3diphy

Maximum likelihood structural phylogenetics by including Foldseek 3Di characters. Supporting Information for Puente-Lelievre et al. 2023n for

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angiosperm-chromosome-number-evolution

Analysis of the rates of chromosome number evolution and lineage diversification in major angiosperm clades.

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lshmm

code to run Li and Stephens

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onekg_analysis

Evaluation of genotype imputation methods using the unified genealogy dataset

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sc2ts

Infer a succinct tree sequence from SARS-COV-2 variation data

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tsimpute

Genome-wide genotype imputation using tree sequences.

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tskit

Population-scale genomics

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AllTheBacteria

Follow up to Grace Blackwell's 661k dataset, for 2023

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atb_analysis

Anaysis of the bacterial genomes in AllTheBacteria

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BDMM-Prime

Modified implementation of the BDMM multi-type birth-death model for BEAST 2.

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CherryML

Scalable Maximum Likelihood Estimation of Phylogenetic Models

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GRAPL

GRAPL: A computational library for nonparametric structural causal modelling, analysis and inference

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hmmlearn

Hidden Markov Models in Python, with scikit-learn like API

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numpy-100

100 numpy exercises (with solutions)

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phylokit

Phylogenetics toolkit for the PyData Ecosystem

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popgen-notes

Population genetics notes

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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 ;)

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pvae

code for "Continuous Hierarchical Representations with Poincaré Variational Auto-Encoders".

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rse-course

Materials for Turing's Research Software Engineering course

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rustlings

:crab: Small exercises to get you used to reading and writing Rust code!

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SINGER

Sampling and inference of genealogies with recombination

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stat_rethinking_2023

Statistical Rethinking Course for Jan-Mar 2023

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tb_genome_analysis

Analysis of whole genome sequences of M. tuberculosis

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ts-mcmc

A simple prototype for using tskit to store phylogenetic MCMC output.

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tskit_arg_visualizer

Interactive visualization method for ancestral recombination graphs

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tsqc

Utilities for evaluating inferred tree sequences

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