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McVean Lab

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  1. mccortex mccortex Public

    De novo genome assembly and multisample variant calling

    C 112 25

  2. treeseq-inference treeseq-inference Public

    Work for the tree sequence inference paper.

    Python 23 9

  3. TreeWAS TreeWAS Public

    R 15 6

  4. Corticall Corticall Public

    Germline DNM caller based on LdBG assembly of pathogens

    Java 8 3

  5. TreeWASDir TreeWASDir Public

    Repository for our manuscript 'Systematic classification of shared components of genetic risk for common human diseases'.

    R 5 2

  6. DEploid DEploid Public

    Forked from DEploid-dev/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 Ma…

    C++ 4 2

Repositories

Showing 10 of 16 repositories
  • msprime Public Forked from tskit-dev/msprime

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

    C 1 GPL-3.0 87 0 0 Updated Jul 17, 2024
  • stdpopsim Public Forked from popsim-consortium/stdpopsim

    A library of standard simulation models for msprime

    Python 0 MIT 93 0 0 Updated Mar 10, 2021
  • treeseq-inference Public

    Work for the tree sequence inference paper.

    Python 23 Apache-2.0 9 6 0 Updated Oct 19, 2020
  • Corticall Public

    Germline DNM caller based on LdBG assembly of pathogens

    Java 8 3 1 0 Updated May 11, 2020
  • tskit-workshop Public

    JupyterHub infrastructure for tskit workshops

    Jupyter Notebook 3 Apache-2.0 3 6 0 Updated Jun 3, 2019
  • mccortex Public

    De novo genome assembly and multisample variant calling

    C 112 MIT 25 27 1 Updated Mar 28, 2019
  • TreeWASDir Public

    Repository for our manuscript 'Systematic classification of shared components of genetic risk for common human diseases'.

    R 5 MIT 2 2 0 Updated Mar 25, 2019
  • mixedIBD-Supplement Public

    Supplementary material for mixedIBD paper

    Jupyter Notebook 0 Apache-2.0 2 0 0 Updated Jan 29, 2019
  • DEploid Public Forked from DEploid-dev/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 infection setting.

    C++ 4 GPL-3.0 10 0 0 Updated Nov 20, 2018
  • DEploid-r Public Forked from DEploid-dev/DEploid-r

    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++ 1 GPL-3.0 3 0 0 Updated Oct 20, 2018
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