hyanwong/unified_genealogy_paper Fork of awohns/unified_genealogy_paper

A Unified Genealogy of Modern and Ancient Humans

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hyanwong/GeneticInheritanceGraphLibrary

Language: Python - Size: 457 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 2 - Forks: 1

hyanwong/what-is-an-arg-paper Fork of tskit-dev/what-is-an-arg-paper

Manuscript and code for the "What is an ARG?" paper

Language: TeX - Size: 6 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

hyanwong/tours Fork of OneZoom/tours

scripts for populating the OneZoom database with tour data

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hyanwong/GARG-workshop-notebooks

Language: Jupyter Notebook - Size: 1000 Bytes - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

hyanwong/mike Fork of Argonum-Clever2/mike

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hyanwong/tutorials Fork of tskit-dev/tutorials

A set of tutorials for msprime and tskit.

Language: Jupyter Notebook - Size: 15.3 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

hyanwong/tskit Fork of tskit-dev/tskit

The tree sequence toolkit

Language: Python - Size: 12.5 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 0 - Forks: 1

hyanwong/tsdate Fork of tskit-dev/tsdate

Infer node ages conditional on a tree sequence topology.

Language: Python - Size: 12.9 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

hyanwong/tsqc Fork of tskit-dev/tsqc

Utilities for evaluating tsinfer inferences

Size: 933 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

hyanwong/vcf-zarr-spec Fork of pystatgen/vcf-zarr-spec

VCF Zarr Specification

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hyanwong/sgkit Fork of pystatgen/sgkit

Scalable genetics toolkit

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hyanwong/tstrait Fork of tskit-dev/tstrait

Quantitative trait simulation for ARGs

Size: 1.57 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

hyanwong/tskit_arg_visualizer Fork of kitchensjn/tskit_arg_visualizer

Interactive visualization method for ancestral recombination graphs stored as tskit tree sequences

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hyanwong/progen-2023 Fork of petrelharp/progen-2023

tskit poster for probgen 2023

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hyanwong/lshmm Fork of astheeggeggs/lshmm

code to run Li and Stephens

Size: 2.96 MB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

hyanwong/uikit-site Fork of uikit/uikit-site

The UIkit documentation and website

Language: Vue - Size: 20.6 MB - Last synced: 11 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

hyanwong/tszip Fork of tskit-dev/tszip

Gzip-like compression for tskit tree sequences

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hyanwong/tsviz Fork of tskit-dev/tsviz

Visualisation tools for tree sequences

Language: Jupyter Notebook - Size: 25.4 KB - Last synced: 11 months ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 1

hyanwong/tsutil

Utility functions for tskit

Language: Python - Size: 6.84 KB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

hyanwong/tspyro

Inferring geography, time (and maybe other stuff) with Pyro and tree sequences

Size: 289 KB - Last synced: 11 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

hyanwong/tskit-paper Fork of tskit-dev/tskit-paper

Size: 3.91 KB - Last synced: 11 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

hyanwong/tsinfer-benchmarking

Language: Python - Size: 5.76 MB - Last synced: 11 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 1

hyanwong/symlink-webpack-plugin Fork of hmsk/symlink-webpack-plugin

🔗 Make symbolic links among files built by Webpack

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hyanwong/tsconvert Fork of tskit-dev/tsconvert

Utilities for converting tree sequences to and from other formats

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hyanwong/treeseq-node-identifiability

Examples and issues to assess identifiability of nodes in an arg / tree sequence

Size: 1.95 KB - Last synced: 11 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

hyanwong/treeseq-inference Fork of mcveanlab/treeseq-inference

Work for the tree sequence inference paper.

Language: Python - Size: 53.5 MB - Last synced: 11 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

hyanwong/treescape Fork of thibautjombart/treescape

Exploring tree diversity

Language: HTML - Size: 20 MB - Last synced: 11 months ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

hyanwong/TreeCmp Fork of TreeCmp/TreeCmp

TreeCmp: comparison of trees in polynomial time

Language: Java - Size: 2.1 MB - Last synced: 11 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

hyanwong/testing_compact_hilbert Fork of pdebuyl/testing_compact_hilbert

Code for testing the compact Hilbert index

Language: Python - Size: 10.7 KB - Last synced: 11 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

hyanwong/sysop-mysql Fork of mihaics/sysop-mysql

dockerized mysql server using phusion/baseimage

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hyanwong/stdpopsim Fork of popsim-consortium/stdpopsim

A library of standard population genetic models

Size: 1.71 MB - Last synced: 11 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

hyanwong/stable Fork of vlshchur/argentum-proof-of-concept

Language: C++ - Size: 27.3 KB - Last synced: 11 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

hyanwong/msprime-1.0-paper Fork of tskit-dev/msprime-1.0-paper

Publication describing msprime 1.0

Language: TeX - Size: 2 MB - Last synced: 11 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

hyanwong/sphinx-argparse Fork of alex-rudakov/sphinx-argparse

Sphinx extension that automatically document argparse commands and options

Size: 271 KB - Last synced: 11 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

hyanwong/SPR-tskit-demo

Some demonstration notebooks for SPR moves on simulated and inferred tree sequences

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hyanwong/SLiM Fork of MesserLab/SLiM

Selection on Linked Mutations: A forward population genetic simulation for studying linkage effects, such as hitchhiking, background selection, and Hill-Robertson interference.

Language: C++ - Size: 24.7 MB - Last synced: 11 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

hyanwong/py-factorgraph Fork of mbforbes/py-factorgraph

Factor graphs and loopy belief propagation implemented in Python

Language: Python - Size: 428 KB - Last synced: 11 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

hyanwong/pyodide Fork of pyodide/pyodide

Pyodide is a Python distribution for the browser and Node.js based on WebAssembly

Size: 15.7 MB - Last synced: 11 months ago - Pushed: almost 1 year ago - Stars: 0 - Forks: 0

hyanwong/pyslim Fork of tskit-dev/pyslim

Tools for dealing with tree sequences coming to and from SLiM.

Size: 12.9 MB - Last synced: 11 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

hyanwong/PhyloParser Fork of sephonlee/PhyloParser

Automatically read tree structure from image format

Size: 125 KB - Last synced: 11 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

hyanwong/phylotastic Fork of phylotastic/phylotastic

Administration, organization and outreach for the Phylotastic project

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hyanwong/OneZoomIdentifiers

A repo to help rework the OneZoom code that matches identifiers from different DB providers

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hyanwong/numpy Fork of numpy/numpy

The fundamental package for scientific computing with Python.

Size: 111 MB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

hyanwong/mplcairo Fork of matplotlib/mplcairo

A (new) cairo backend for Matplotlib.

Language: C++ - Size: 631 KB - Last synced: 11 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

hyanwong/gPb-GSoC Fork of HiDiYANG/gPb-GSoC

Language: C++ - Size: 119 MB - Last synced: 11 months ago - Pushed: over 9 years ago - Stars: 1 - Forks: 2

hyanwong/molecular-sample-dating

Methods for dating ancient samples using tree sequence methods

Language: Jupyter Notebook - Size: 153 KB - Last synced: 11 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

hyanwong/kastore Fork of tskit-dev/kastore

The key-array store for read-only numerical data.

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hyanwong/jlite-workshop

Language: Jupyter Notebook - Size: 72.3 KB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

hyanwong/jupyter-book Fork of executablebooks/jupyter-book

Build interactive, publication-quality documents from Jupyter Notebooks

Size: 62.5 MB - Last synced: 11 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

hyanwong/indexed_bzip2 Fork of mxmlnkn/indexed_bzip2

Fast random access of bzip2 files in Python

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hyanwong/genealogy_workshop

Language: Jupyter Notebook - Size: 154 MB - Last synced: 11 months ago - Pushed: 12 months ago - Stars: 1 - Forks: 0

hyanwong/ftprime Fork of ashander/ftprime

Forward-time simulation of the msprime data structure (for development)

Language: Python - Size: 1.17 MB - Last synced: 11 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

hyanwong/fastARG Fork of lh3/fastARG

Fast heuristic ARG construction

Language: C - Size: 41 KB - Last synced: 11 months ago - Pushed: over 7 years ago - Stars: 1 - Forks: 0

hyanwong/eol_php_code Fork of EOL/deprecated_eol_php_code

Language: PHP - Size: 48.5 MB - Last synced: 11 months ago - Pushed: over 9 years ago - Stars: 0 - Forks: 0

hyanwong/EOL-thumbnail-viewer

A single page that shows a set of 'best' Encyclopedia of Life thumbnails

Language: HTML - Size: 5.86 KB - Last synced: 11 months ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

hyanwong/ARG-assess-via-imputation

Size: 1.95 KB - Last synced: 11 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

hyanwong/docker-nginx Fork of madharjan/docker-nginx

Docker container for Nginx

Size: 46.9 KB - Last synced: 11 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

hyanwong/EoL-simple-ecards

A simple ecards script of the Encyclopaedia of Life

Language: Perl - Size: 137 KB - Last synced: 11 months ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

hyanwong/dynamic-ARG-viz

Draft repo for creating graph-like representations of succinct tree sequences, with user interaction

Size: 1.95 KB - Last synced: 11 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

hyanwong/docker-base Fork of madharjan/docker-base

Docker baseimage based on phusion/baseimage-docker

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hyanwong/canvas2svg Fork of gliffy/canvas2svg

Language: JavaScript - Size: 429 KB - Last synced: 11 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

hyanwong/cyvcf2 Fork of brentp/cyvcf2

cython + htslib == fast VCF and BCF processing

Size: 14.1 MB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

hyanwong/butterfly-image-extraction

Language: Python - Size: 8.64 MB - Last synced: 11 months ago - Pushed: over 9 years ago - Stars: 1 - Forks: 1

hyanwong/bmrc-containers-teaching Fork of bmrc-oxford/bmrc-containers-teaching

Size: 5.86 KB - Last synced: 11 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

hyanwong/argweaver Fork of CshlSiepelLab/argweaver

Sampling and manipulating genome-wide ancestral recombination graphs (ARGs)

Size: 4.34 MB - Last synced: 11 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

hyanwong/argentum Fork of nvalimak/argentum

Argentum

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hyanwong/100kG-testing

Language: Jupyter Notebook - Size: 176 KB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

hyanwong/argbd Fork of a-ignatieva/argbd

Size: 789 KB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

hyanwong/tree-build Fork of OneZoom/tree-build

Scripts for assembling the tree, metadata and downstream data products such as popularity and popular images

Language: Python - Size: 764 KB - Last synced: 11 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

hyanwong/demesdraw Fork of grahamgower/demesdraw

Drawing functions for Demes demographic models

Size: 101 MB - Last synced: 11 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

hyanwong/workshop-pages

Oxford statgen genealogy workshop jupyterlite instance

Language: Jupyter Notebook - Size: 6.44 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

hyanwong/sc2ts-paper Fork of jeromekelleher/sc2ts-paper

Language: Python - Size: 10.1 MB - Last synced: 11 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

hyanwong/sc2ts Fork of jeromekelleher/sc2ts

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

Size: 4.97 MB - Last synced: 11 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

hyanwong/pages

Language: Jupyter Notebook - Size: 14.5 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

hyanwong/OZtree Fork of OneZoom/OZtree

OneZoom Tree of Life Explorer

Language: HTML - Size: 290 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

hyanwong/tskit-site Fork of tskit-dev/tskit-site

tskit website

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hyanwong/tsinfer Fork of tskit-dev/tsinfer

Infer a tree sequence from genetic variation data

Language: Python - Size: 4.55 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 0

hyanwong/tsdate_paper Fork of awohns/unified_genealogy_paper

Evaluation of tsdate algorithm

Language: Python - Size: 2.14 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

hyanwong/msprime Fork of tskit-dev/msprime

A reimplementation of Hudson's classical ms simulator for modern data sets.

Language: C - Size: 15.1 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

hyanwong/administrative Fork of tskit-dev/administrative

project management documents and discussions for tskit development

Size: 5.14 MB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

hyanwong/uikit Fork of uikit/uikit

A lightweight and modular front-end framework for developing fast and powerful web interfaces

Language: CSS - Size: 42.7 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

hyanwong/eol Fork of EOL/deprecated_eol

Encyclopedia of Life

Language: Ruby - Size: 171 MB - Last synced: 11 months ago - Pushed: about 9 years ago - Stars: 0 - Forks: 0