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)

Peer review:

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6 exports 0.00 score 44 dependencies 30 scripts 265 downloads

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

Exports:optimize_bigMoptimize_moptimize_nvis_depthvis_locivis_snps

Dependencies:apecliclustercolorspacedigestdplyrfansifarvergenericsggplot2ggridgesgluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmemusemgcvmunsellnlmepermutepillarpinfsc50pkgconfigR6RColorBrewerRcpprlangscalesstringistringrtibbletidyselectutf8vcfRvctrsveganviridisLitewithr