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RADstackshelpR  

Optimize the De Novo Stacks Pipeline via R
View on CRAN: Click here


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

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

Install by package version:
library("remotes")
install_version("RADstackshelpR", "0.1.0")



Attach the package and use:
library("RADstackshelpR")
Maintained by
Devon DeRaad
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-08-19
Latest Update: 2021-08-19
Description:
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) () 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) () which establishes clear recommendations for optimizing the parameters 'm', 'M', and 'n', during the process of assembling loci.
How to cite:
Devon DeRaad (2021). RADstackshelpR: Optimize the De Novo Stacks Pipeline via R. R package version 0.1.0, https://cran.r-project.org/web/packages/RADstackshelpR. Accessed 04 Jun. 2026.
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Complete documentation for RADstackshelpR
Functions, R codes and Examples using the RADstackshelpR R package
Some associated functions: optimize_bigM . optimize_m . optimize_n . vis_depth . vis_loci . vis_snps . 
Some associated R codes: optimize_bigM.R . optimize_m.R . optimize_n.R . vis_depth.R . vis_loci.R . vis_snps.R .  Full RADstackshelpR package functions and examples
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