DEploid.utils: 'DEploid' Data Analysis and Results Interpretation

'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.

Version: 0.0.1
Depends: R (≥ 3.1.0)
Imports: Rcpp (≥ 0.11.2), scales (≥ 0.4.0), magrittr (≥ 1.5), combinat
LinkingTo: Rcpp
Suggests: knitr, rmarkdown (≥ 1.6), circlize, testthat (≥ 0.9.0)
Published: 2024-12-19
DOI: 10.32614/CRAN.package.DEploid.utils
Author: Joe Zhu ORCID iD [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>
License: Apache License (≥ 2)
NeedsCompilation: yes
Materials: README NEWS
CRAN checks: DEploid.utils results

Documentation:

Reference manual: DEploid.utils.pdf

Downloads:

Package source: DEploid.utils_0.0.1.tar.gz
Windows binaries: r-devel: DEploid.utils_0.0.1.zip, r-release: DEploid.utils_0.0.1.zip, r-oldrel: DEploid.utils_0.0.1.zip
macOS binaries: r-release (arm64): DEploid.utils_0.0.1.tgz, r-oldrel (arm64): DEploid.utils_0.0.1.tgz, r-release (x86_64): DEploid.utils_0.0.1.tgz, r-oldrel (x86_64): DEploid.utils_0.0.1.tgz

Reverse dependencies:

Reverse depends: DEploid

Linking:

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