DEploid: Deconvolute Mixed Genomes with Unknown Proportions

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.

Version:	0.5.7
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)
LinkingTo:	Rcpp
Suggests:	knitr, testthat (≥ 0.9.0)
Published:	2025-01-20
DOI:	10.32614/CRAN.package.DEploid
Author:	Joe Zhu [aut, cre], 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 at gmail.com>
BugReports:	https://github.com/DEploid-dev/DEploid-r/issues
License:	GPL (≥ 3)
URL:	https://github.com/DEploid-dev/DEploid-r
NeedsCompilation:	yes
Citation:	DEploid citation info
Materials:	README
CRAN checks:	DEploid results

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