polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

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, or genotypes sampled from those probabilties, can then be exported for downstream analysis. 'polyRAD' is described by Clark et al. (2019) <doi:10.1534/g3.118.200913>.

Version: 1.1
Imports: fastmatch, pcaMethods, methods, Rcpp
LinkingTo: Rcpp
Suggests: rrBLUP, Rsamtools, GenomeInfoDb, Biostrings, GenomicRanges, VariantAnnotation, SummarizedExperiment, S4Vectors, IRanges, BiocGenerics, knitr, rmarkdown, GenomicFeatures, qqman
Published: 2019-06-04
Author: Lindsay V. Clark ORCID iD [aut, cre], U.S. National Science Foundation [fnd]
Maintainer: Lindsay V. Clark <lvclark at illinois.edu>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://github.com/lvclark/polyRAD
NeedsCompilation: yes
Citation: polyRAD citation info
Materials: NEWS
CRAN checks: polyRAD results


Reference manual: polyRAD.pdf
Vignettes: polyRAD Tutorial
Package source: polyRAD_1.1.tar.gz
Windows binaries: r-devel: polyRAD_1.1.zip, r-devel-gcc8: polyRAD_1.1.zip, r-release: polyRAD_1.1.zip, r-oldrel: polyRAD_1.1.zip
OS X binaries: r-release: polyRAD_1.1.tgz, r-oldrel: polyRAD_1.1.tgz
Old sources: polyRAD archive


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