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polyRAD  

Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("polyRAD", "2.0.0")



Attach the package and use:
library("polyRAD")
Maintained by
Lindsay V. Clark
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-08-02
Latest Update: 2022-11-06
Description:
Read depth data from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian probability estimates of genotypes in polyploids or diploids. The genotype probabilities, posterior mean genotypes, or most probable genotypes can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2019) , and the Hind/He statistic for marker filtering is described by Clark et al. (2022) . A variant calling pipeline for highly duplicated genomes is also included and is described by Clark et al. (2020, Version 1) .
How to cite:
Lindsay V. Clark (2018). polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids. R package version 2.0.0, https://cran.r-project.org/web/packages/polyRAD. Accessed 05 Jan. 2025.
Previous versions and publish date:
0.5-0 (2018-08-02 17:30), 1.0 (2018-11-20 00:30), 1.1 (2019-06-04 22:00), 1.2 (2020-05-12 23:10), 1.3 (2021-01-06 08:30), 1.4 (2021-03-23 00:00), 1.5 (2021-09-03 00:20), 1.6 (2022-02-15 22:30)
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