Package: RADstackshelpR 0.1.0

Devon DeRaad

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.

Authors:Devon DeRaad [aut, cre]

RADstackshelpR_0.1.0.tar.gz
RADstackshelpR_0.1.0.tar.gz(r-4.5-noble)RADstackshelpR_0.1.0.tar.gz(r-4.4-noble)
RADstackshelpR_0.1.0.tgz(r-4.4-emscripten)RADstackshelpR_0.1.0.tgz(r-4.3-emscripten)
RADstackshelpR.pdf |RADstackshelpR.html
RADstackshelpR/json (API)

# Install 'RADstackshelpR' in R:
install.packages('RADstackshelpR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.70 score 30 scripts 177 downloads 6 exports 44 dependencies

Last updated 3 years agofrom:c8ab76ab58. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 14 2024
R-4.5-linuxNOTEDec 14 2024

Exports:optimize_bigMoptimize_moptimize_nvis_depthvis_locivis_snps

Dependencies:apecliclustercolorspacedigestdplyrfansifarvergenericsggplot2ggridgesgluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmemusemgcvmunsellnlmepermutepillarpinfsc50pkgconfigR6RColorBrewerRcpprlangscalesstringistringrtibbletidyselectutf8vcfRvctrsveganviridisLitewithr

Reproducible example

Rendered fromreproducible.vignette.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2021-08-19
Started: 2021-08-19