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
NeedsCompilation: yes
Packaged: 2025-01-20 02:29:18 UTC; rstudio
Author: Joe Zhu [aut, cre] (<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>
Repository: CRAN
Date/Publication: 2025-01-20 03:20:02 UTC
Built: R 4.6.0; x86_64-apple-darwin20; 2026-04-30 10:02:32 UTC; unix
Archs: DEploid.so.dSYM
