updog

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.

Last 30 days

This package has been downloaded 291 times in the last 30 days. Enough downloads to make a small wave in the niche community. The curiosity is spreading! The following heatmap shows the distribution of downloads per day. Yesterday, it was downloaded 17 times.

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Last 365 days

This package has been downloaded 4,835 times in the last 365 days. Now we’re talking! This work is officially 'heard of in academic circles', just like those wild research papers on synthetic bananas. The day with the most downloads was Jan 30, 2025 with 80 downloads.

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