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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
      •92•1•0•0•Updated Jul 17, 2024Jul 17, 2024

    • stdpopsim

      Public
      A library of standard simulation models for msprime
      Python
      •
      MIT License
      •94•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
      linksgenometraversalconnectivityjava-apivariant-callingcortexde-bruijn-graphsdenovo-assemblyclass-library
      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-callingkmercortexgenome-analysisgenome-assemblyde-bruijn-graphsgenome-graphcontigs
      C
      •
      MIT License
      •24•112•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 modifi…
      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 …
      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•16•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