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  [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: not available, 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 |
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