updog: Flexible Genotyping for Polyploids
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.
| Version: | 2.1.5 |
| Depends: | R (≥ 3.4.0) |
| Imports: | Rcpp (≥ 0.12.16), RcppArmadillo, assertthat, ggplot2, reshape2, foreach, future, doFuture, doRNG, methods, iterators |
| LinkingTo: | Rcpp, RcppArmadillo |
| Suggests: | covr, testthat, SuppDists, knitr, rmarkdown, VariantAnnotation, GenomicRanges, S4Vectors, IRanges |
| Published: | 2023-11-29 |
| Author: | David Gerard 
[aut, cre] |
| Maintainer: | David Gerard <gerard.1787 at gmail.com> |
| BugReports: | https://github.com/dcgerard/updog/issues |
| License: | GPL-3 |
| URL: | https://github.com/dcgerard/updog/ |
| NeedsCompilation: | yes |
| Citation: | updog citation info |
| Materials: | README NEWS |
| CRAN checks: | updog results |
Documentation:
| Reference manual: | updog.pdf |
| Vignettes: |
Genotyping Many SNPs with multidog() Oracle Calculations Simulate Next-Generation Sequencing Data Example Use of Updog |
Downloads:
| Package source: | updog_2.1.5.tar.gz |
| Windows binaries: | r-devel: updog_2.1.5.zip, r-release: updog_2.1.5.zip, r-oldrel: updog_2.1.5.zip |
| macOS binaries: | r-release (arm64): updog_2.1.5.tgz, r-oldrel (arm64): updog_2.1.5.tgz, r-release (x86_64): updog_2.1.5.tgz, r-oldrel (x86_64): updog_2.1.5.tgz |
| Old sources: | updog archive |
Reverse dependencies:
| Reverse imports: | hwep |
| Reverse suggests: | ldsep, mappoly, polymapR |
Linking:
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