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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 7 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 1

Repositories

Showing 10 of 16 repositories
  • stdpopsim Public Forked from popsim-consortium/stdpopsim

    A library of standard simulation models for msprime

    mcveanlab/stdpopsim’s past year of commit activity
    Python 0 MIT 86 0 0 Updated Mar 10, 2021
  • msprime Public Forked from tskit-dev/msprime

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

    mcveanlab/msprime’s past year of commit activity
    C 1 GPL-3.0 84 0 0 Updated Mar 3, 2021
  • treeseq-inference Public

    Work for the tree sequence inference paper.

    mcveanlab/treeseq-inference’s past year of commit activity
    Python 23 Apache-2.0 9 8 0 Updated Oct 19, 2020
  • Corticall Public

    Germline DNM caller based on LdBG assembly of pathogens

    mcveanlab/Corticall’s past year of commit activity
    Java 7 3 1 0 Updated May 11, 2020
  • tskit-workshop Public

    JupyterHub infrastructure for tskit workshops

    mcveanlab/tskit-workshop’s past year of commit activity
    Jupyter Notebook 3 Apache-2.0 3 6 0 Updated Jun 3, 2019
  • mccortex Public

    De novo genome assembly and multisample variant calling

    mcveanlab/mccortex’s past year of commit activity
    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'.

    mcveanlab/TreeWASDir’s past year of commit activity
    R 5 MIT 2 2 0 Updated Mar 25, 2019
  • mixedIBD-Supplement Public

    Supplementary material for mixedIBD paper

    mcveanlab/mixedIBD-Supplement’s past year of commit activity
    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.

    mcveanlab/DEploid’s past year of commit activity
    C++ 4 GPL-3.0 9 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…

    mcveanlab/DEploid-r’s past year of commit activity
    C++ 1 GPL-3.0 3 0 0 Updated Oct 20, 2018
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