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DEploid  

Deconvolute Mixed Genomes with Unknown Proportions
View on CRAN: Click here


Download and install DEploid package within the R console
Install from CRAN:
install.packages("DEploid")

Install from Github:
library("remotes")
install_github("cran/DEploid")

Install by package version:
library("remotes")
install_version("DEploid", "0.5.7")



Attach the package and use:
library("DEploid")
Maintained by
Joe Zhu
[Scholar Profile | Author Map]
First Published: 2016-11-25
Latest Update: 2024-10-14
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.
How to cite:
Joe Zhu (2016). DEploid: Deconvolute Mixed Genomes with Unknown Proportions. R package version 0.5.7, https://cran.r-project.org/web/packages/DEploid. Accessed 17 Feb. 2025.
Previous versions and publish date:
0.3.2 (2016-11-25 19:47), 0.4.1 (2017-07-24 21:21), 0.4.2 (2017-08-09 09:57), 0.4.3 (2017-08-09 22:58), 0.4.4 (2017-09-01 05:09), 0.5.0 (2018-05-18 05:28), 0.5.1 (2018-10-21 17:40), 0.5.2 (2018-10-23 18:50), 0.5.3 (2020-04-22 00:20), 0.5.4 (2024-10-14 10:40), 0.5.6 (2024-12-23 16:30)
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Full DEploid package functions and examples
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