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updog  

Flexible Genotyping for Polyploids
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("updog", "2.1.6")



Attach the package and use:
library("updog")
Maintained by
David Gerard
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-07-10
Latest Update: 2023-11-29
Description:
Implements empirical Bayes approaches to genotype polyploids from next generation sequencing data while accounting for allele bias, overdispersion, and sequencing error. The main functions are flexdog() and multidog(), which allow the specification of many different genotype distributions. Also provided are functions to simulate genotypes, rgeno(), and read-counts, rflexdog(), as well as functions to calculate oracle genotyping error rates, oracle_mis(), and correlation with the true genotypes, oracle_cor(). These latter two functions are useful for read depth calculations. Run browseVignettes(package = "updog") in R for example usage. See Gerard et al. (2018) <doi:10.1534/genetics.118.301468> and Gerard and Ferrao (2020) <doi:10.1093/bioinformatics/btz852> for details on the implemented methods.
How to cite:
David Gerard (2018). updog: Flexible Genotyping for Polyploids. R package version 2.1.6, https://cran.r-project.org/web/packages/updog. Accessed 05 Jun. 2026.
Previous versions and publish date:
1.0.0 (2018-07-10 18:20), 1.0.1 (2018-07-27 19:50), 1.1.0 (2019-07-31 20:30), 1.1.1 (2019-09-10 01:30), 1.1.3 (2019-11-21 17:30), 1.2.0 (2020-01-28 17:30), 2.0.2 (2020-07-21 10:40), 2.1.1 (2021-10-26 01:10), 2.1.2 (2022-01-24 22:50), 2.1.3 (2022-10-18 10:00), 2.1.4 (2023-11-17 06:00), 2.1.5 (2023-11-29 16:50), 2.1.6 (2025-09-24 07:10)
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