RADstackshelpR: Optimize the De Novo Stacks Pipeline via R

Offers a handful of useful wrapper functions which streamline the reading, analyzing, and visualizing of variant call format (vcf) files in R. This package was designed to facilitate an explicit pipeline for optimizing Stacks (Rochette et al., 2019) (<doi:10.1111/mec.15253>) parameters during de novo (without a reference genome) assembly and variant calling of restriction-enzyme associated DNA sequence (RADseq) data. The pipeline implemented here is based on the 2017 paper "Lost in Parameter Space" (Paris et al., 2017) (<doi:10.1111/2041-210X.12775>) which establishes clear recommendations for optimizing the parameters 'm', 'M', and 'n', during the process of assembling loci.

Version:	0.1.0
Imports:	vcfR, ggplot2, ggridges, gridExtra
Suggests:	knitr, rmarkdown
Published:	2021-08-19
DOI:	10.32614/CRAN.package.RADstackshelpR
Author:	Devon DeRaad [aut, cre]
Maintainer:	Devon DeRaad <devonderaad at gmail.com>
License:	MIT + file LICENSE
NeedsCompilation:	no
Materials:	README
CRAN checks:	RADstackshelpR results

Documentation:

Reference manual:	RADstackshelpR.pdf
Vignettes:	Reproducible example

Downloads:

Package source:	RADstackshelpR_0.1.0.tar.gz
Windows binaries:	r-devel: RADstackshelpR_0.1.0.zip, r-release: RADstackshelpR_0.1.0.zip, r-oldrel: RADstackshelpR_0.1.0.zip
macOS binaries:	r-release (arm64): RADstackshelpR_0.1.0.tgz, r-oldrel (arm64): RADstackshelpR_0.1.0.tgz, r-release (x86_64): RADstackshelpR_0.1.0.tgz, r-oldrel (x86_64): RADstackshelpR_0.1.0.tgz

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