Package: DEploid
Type: Package
Title: Deconvolute Mixed Genomes with Unknown Proportions
Version: 0.5.7
Authors@R: c(
    person("Joe", "Zhu", , "sha.joe.zhu@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-7566-2787")),
    person('Jacob', 'Almagro-Garcia', role=c('aut')),
    person('Gil', 'McVean', role=c('aut')),
    person('University of Oxford', '', role=c('cph')),
    person('Yinghan', 'Liu', role=c('ctb')),
    person('CodeCogs', 'Zyba Ltd', role=c('com', "cph")),
    person('Deepak', 'Bandyopadhyay', role=c('com', "cph")),
    person('Lutz', 'Kettner', role=c('com', "cph"))
    )
Description: Traditional phasing programs are limited to diploid
        organisms. Our method modifies Li and Stephens algorithm with
        Markov chain Monte Carlo (MCMC) approaches, and builds a
        generic framework that allows haplotype searches in a multiple
        infection setting. This package is primarily developed as part
        of the Pf3k project, which is a global collaboration using the
        latest sequencing technologies to provide a high-resolution
        view of natural variation in the malaria parasite Plasmodium
        falciparum. Parasite DNA are extracted from patient blood
        sample, which often contains more than one parasite strain,
        with unknown proportions. This package is used for
        deconvoluting mixed haplotypes, and reporting the mixture
        proportions from each sample.
URL: https://github.com/DEploid-dev/DEploid-r
BugReports: https://github.com/DEploid-dev/DEploid-r/issues
License: GPL (>= 3)
Depends: R (>= 3.1.0), DEploid.utils (>= 0.0.1)
Imports: Rcpp (>= 0.11.2), scales (>= 0.4.0), plotly (>= 4.7.1),
        magrittr (>= 1.5), rmarkdown(>= 1.6), htmlwidgets (>= 1.0)
Suggests: knitr, testthat (>= 0.9.0)
VignetteBuilder: knitr
LinkingTo: Rcpp
RoxygenNote: 7.3.2
Encoding: UTF-8
Date: 2024-12-22
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libssl-dev
Repository: https://plasmogenepi.r-universe.dev
Date/Publication: 2025-01-21 04:56:27 UTC
RemoteUrl: https://github.com/DEploid-dev/DEploid-r
RemoteRef: HEAD
RemoteSha: 13f0fe1299511645d21e4c2558e85602c6cfc0f9
NeedsCompilation: yes
Packaged: 2026-06-17 10:20:41 UTC; root
Author: Joe Zhu [aut, cre] (ORCID: <https://orcid.org/0000-0001-7566-2787>),
  Jacob Almagro-Garcia [aut],
  Gil McVean [aut],
  University of Oxford [cph],
  Yinghan Liu [ctb],
  CodeCogs Zyba Ltd [com, cph],
  Deepak Bandyopadhyay [com, cph],
  Lutz Kettner [com, cph]
Maintainer: Joe Zhu <sha.joe.zhu@gmail.com>