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    16 repositories

    • msprime

      Public
      A reimplementation of Hudson's classical ms simulator for modern data sets.
      C
      •
      GNU General Public License v3.0
      •88•1•0•0•Updated Jul 17, 2024Jul 17, 2024

    • stdpopsim

      Public
      A library of standard simulation models for msprime
      Python
      •
      MIT License
      •87•0•0•0•Updated Mar 10, 2021Mar 10, 2021

    • treeseq-inference

      Public
      Work for the tree sequence inference paper.
      Python
      •
      Apache License 2.0
      •9•23•6•0•Updated Oct 19, 2020Oct 19, 2020

    • Corticall

      Public
      Germline DNM caller based on LdBG assembly of pathogens
      linksgenometraversalconnectivityvariant-callingdenovo-assemblyclass-libraryjava-apicortexde-bruijn-graphs
      Java
      •
      Other
      •3•8•1•0•Updated May 11, 2020May 11, 2020

    • tskit-workshop

      Public
      JupyterHub infrastructure for tskit workshops
      Jupyter Notebook
      •
      Apache License 2.0
      •3•3•6•0•Updated Jun 3, 2019Jun 3, 2019

    • mccortex

      Public
      De novo genome assembly and multisample variant calling
      genomicsvariant-callinggenome-analysisgenome-graphcontigskmercortexgenome-assemblyde-bruijn-graphs
      C
      •
      MIT License
      •25•113•27•1•Updated Mar 28, 2019Mar 28, 2019

    • TreeWASDir

      Public
      Repository for our manuscript 'Systematic classification of shared components of genetic risk for common human diseases'.
      R
      •
      MIT License
      •2•5•2•0•Updated Mar 25, 2019Mar 25, 2019

    • mixedIBD-Supplement

      Public
      Supplementary material for mixedIBD paper
      Jupyter Notebook
      •
      Apache License 2.0
      •2•0•0•0•Updated Jan 29, 2019Jan 29, 2019

    • DEploid

      Public
      dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.
      C++
      •
      GNU General Public License v3.0
      •10•4•0•0•Updated Nov 20, 2018Nov 20, 2018

    • DEploid-r

      Public
      An R interface for dEploid. dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infe…
      C++
      •
      GNU General Public License v3.0
      •3•1•0•0•Updated Oct 20, 2018Oct 20, 2018

    • schmidtWorkshop

      Public
      Code used in Scmidt Science Fellowship workshop
      Jupyter Notebook
      •
      MIT License
      •2•1•0•0•Updated Jul 25, 2018Jul 25, 2018

    • schmidtWorkshop-docker

      Public
      Builds a docker image out of the schmidtWorkshop repo
      Dockerfile
      •
      MIT License
      •2•0•0•0•Updated Jul 25, 2018Jul 25, 2018

    • TreeWAS

      Public
      R
      •
      MIT License
      •6•15•5•0•Updated Oct 16, 2017Oct 16, 2017

    • bdiBeamer

      Public
      TeX
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 22, 2017Jun 22, 2017

    • PfDeconv

      Public
      PfDeconv is now renamed as DEploid.
      0•0•0•0•Updated Jul 29, 2016Jul 29, 2016

    • PacBio

      Public
      Assessments of PacBio datasets
      Perl
      •1•0•0•0•Updated Oct 17, 2014Oct 17, 2014