Package: DEploid.utils
Title: 'DEploid' Data Analysis and Results Interpretation
Version: 0.0.1
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: 'DEploid' (Zhu et.al. 2018 <doi:10.1093/bioinformatics/btx530>)
    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. This package provides R functions
    to support data analysis and results interpretation.  
Depends: R (>= 3.1.0)
Imports: Rcpp (>= 0.11.2), scales (>= 0.4.0), magrittr (>= 1.5),
        combinat
Suggests: knitr, rmarkdown(>= 1.6), circlize, testthat (>= 0.9.0)
LinkingTo: Rcpp
RoxygenNote: 7.3.2
Encoding: UTF-8
Date: 2024-11-18
License: Apache License (>= 2)
NeedsCompilation: yes
Packaged: 2024-12-18 12:02:05 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: 2024-12-19 16:00:18 UTC
Built: R 4.6.0; x86_64-apple-darwin20; 2026-04-27 16:13:21 UTC; unix
Archs: DEploid.utils.so.dSYM
