Repositories list

• 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…

  hmmparasitesmalaria+ 5phasingcranmcmcdeconvoluting-mixed-genomesunknown-proportions

  R

  •

  GNU General Public License v3.0

  •3•1•11•0•Updated Jan 21, 2025Jan 21, 2025

• 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.

  parasitesmalariaphasing+ 4hmm-modelmcmcdeconvoluting-mixed-genomesunknown-proportions

  C++

  •

  GNU General Public License v3.0

  •10•20•22•0•Updated Jan 20, 2025Jan 20, 2025

• DEploid.utils

  Public
  R

  •

  Apache License 2.0

  •1•1•2•0•Updated Dec 23, 2024Dec 23, 2024

• DEploid-vcf-lib

  Public
  C++

  •

  Apache License 2.0

  •0•1•2•0•Updated Dec 23, 2024Dec 23, 2024

• DEploid-Bestpractices-github-actions

  Public
  Apache License 2.0

  •0•0•2•0•Updated Jan 10, 2021Jan 10, 2021

• deploid-dev.github.io

  Public
  0•0•0•0•Updated Jun 6, 2020Jun 6, 2020

• DEploid-Lasso-lib

  Public
  R

  •

  Apache License 2.0

  •1•0•0•0•Updated Oct 31, 2019Oct 31, 2019

• DEploid-Bestpractices-Benchmark-in_silico_field

  Public
  Shell

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  Apache License 2.0

  •0•0•0•0•Updated Aug 4, 2019Aug 4, 2019

• DEploid-Data-Benchmark-in_silico_field

  Public
  R

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  Apache License 2.0

  •1•0•2•0•Updated Aug 4, 2019Aug 4, 2019

• DEploid-Data-Benchmark-in_silico_lab_mixed_4s

  Public
  R

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  Apache License 2.0

  •1•0•0•0•Updated Aug 4, 2019Aug 4, 2019

• mixedIBD

  Public
  TeX

  •0•0•0•0•Updated Jun 26, 2019Jun 26, 2019

• README

  Public
  DEploid-dev README

  0•0•0•0•Updated Dec 12, 2018Dec 12, 2018

• DEploid-Bestpractices-Benchmark-mixed4s

  Public
  Shell

  •1•0•0•0•Updated Nov 29, 2018Nov 29, 2018

• DEploid-py

  Public
  Python 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 in…

  C++

  •

  GNU General Public License v3.0

  •0•0•3•0•Updated Nov 15, 2018Nov 15, 2018

• DEploid-Supplementary-Materials

  Public
  R

  •0•0•0•0•Updated May 3, 2018May 3, 2018

• DEploid-ShinyApp

  Public
  R

  •

  GNU General Public License v3.0

  •0•0•7•0•Updated Aug 15, 2017Aug 15, 2017

• dEploidPaper

  Public
  TeX

  •0•0•2•0•Updated Jul 20, 2017Jul 20, 2017