Package: updog Title: Flexible Genotyping for Polyploids Version: 2.1.7 Authors@R: person("David", "Gerard", email = "gerard.1787@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9450-5023")) 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) and Gerard and Ferrao (2020) for details on the implemented methods. Depends: R (>= 3.4.0) License: GPL (>= 3) BugReports: https://github.com/dcgerard/updog/issues URL: https://dcgerard.github.io/updog/ Encoding: UTF-8 LazyData: true RoxygenNote: 7.3.3 LinkingTo: Rcpp, RcppArmadillo Imports: Rcpp (>= 0.12.16), RcppArmadillo, assertthat, ggplot2, reshape2, foreach, future, doFuture, doRNG, methods, iterators, parallelly Suggests: covr, testthat (>= 3.0.0), knitr, rmarkdown, VariantAnnotation, GenomicRanges, S4Vectors, IRanges VignetteBuilder: knitr Config/testthat/edition: 3 Config/pak/sysreqs: libicu-dev Repository: https://dcgerard.r-universe.dev Date/Publication: 2026-03-17 16:54:46 UTC RemoteUrl: https://github.com/dcgerard/updog RemoteRef: HEAD RemoteSha: 04e8c4243f288c8bac92cf8df52141a28dcb2171 NeedsCompilation: yes Packaged: 2026-06-24 08:57:23 UTC; root Author: David Gerard [aut, cre] (ORCID: ) Maintainer: David Gerard