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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.\n\n\nInstallation\n------------\n\nIt is recommended to use the current CRAN version. It can be installed from within R using\n\n```R\n\u003e install.packages('DEploid')\n```\n\nFor the developing version, please install Rcpp package first. From the R-console, type\n\n```R\n\u003e install.packages(\"Rcpp\")\n```\n\n(NOTE: If you are using Windows, please install `Rtools` from [https://cran.r-project.org/bin/windows/Rtools/](https://cran.r-project.org/bin/windows/Rtools/))\n\nthen\n\n```R\n\u003e install.packages(\"devtools\")\n\u003e library(devtools)\n\u003e install_github(\"mcveanlab/DEploid-r\")\n```\n\nUsage\n-----\n\nPlease refer to the help page and examples for each function. For example,\n```R\n\u003e library(DEploid)\n\u003e ?dEploid\n\u003e ?plotProportions\n```\n\nLicence\n-------\n\nYou can freely use all code in this project under the conditions of the GNU GPL Version 3 or later.\n\n\nCitation\n--------\n\nCitation\n--------\n\nIf you use `dEploid` with the flag `-ibd`, please cite the following paper:\n\nZhu, J. S., J. A. Hendry, J. Almagro-Garcia, R. D. Pearson, R. Amato, A. Miles, D. J. Weiss, T. C. D. Lucas, M. Nguyen, P. W. Gething, D. Kwiatkowski, G. McVean, and for the Pf3k Project. (2018) The origins and relatedness structure of mixed infections vary with local prevalence of *P. falciparum* malaria. *eLife*, 40845, doi: https://doi.org/10.7554/eLife.40845.\n\n\nIf you use `dEploid` in your work, please cite the program:\n\nZhu, J. S., J. A. Garcia, G. McVean. (2018) Deconvolution of multiple infections in *Plasmodium falciparum* from high throughput sequencing data. *Bioinformatics* 34(1), 9-15. doi: https://doi.org/10.1093/bioinformatics/btx530.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdeploid-dev%2Fdeploid-r","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdeploid-dev%2Fdeploid-r","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdeploid-dev%2Fdeploid-r/lists"}