In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

description <- readLines("DESCRIPTION")
rvers <- stringr::str_match(grep("R \\(", description, value = TRUE), "[0-9]{1,4}\\.[0-9]{1,4}\\.[0-9]{1,4}")[1,1]
version <- gsub(" ", "", gsub("Version:", "", grep("Version:", description, value = TRUE)))

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

---

radiator: an R package for RADseq Data Exploration, Manipulation and Visualization

Most genomic analysis look for patterns and trends with various statistics. Bias, noise and outliers can have bounded influence on estimators and interfere with polymorphism discovery. Avoid bad data exploration and control the impact of filters on your downstream genetic analysis. Use radiator to: import, explore, manipulate, visualize, filter, impute and export your GBS/RADseq data.

radiator is designed and optimized for fast computations using Genomic Data Structure GDS file format and data science packages in tidyverse. radiator handles VCF files with millions of SNPs and files of several GB.

Installation

To try out the dev version of radiator, copy/paste the code below:

if (!require("pak")) install.packages("pak")
pak::pkg_install("thierrygosselin/radiator")
library(radiator)

To minimize dependencies, just the basic required packages are installed with the command above. If you want the full suits of functions and don't want to be preoccupied, run:

radiator::radiator_pkg_install() # that's it. It will update, when necessary, radiator.

Computer setup and troubleshooting vignette

Learning radiator

Overview of features

Vignettes

Citation:

To get the citation, inside R:

citation("radiator")

Life cycle

radiator is maturing, but in order to make the package better, changes are inevitable. Experimental functions will change, argument names will change.

• Philosophy, major changes and deprecated functions/arguments (link).
• changelog, versions, new features and bug history
• issues
• contributions

thierrygosselin/radiator documentation built on May 5, 2024, 5:12 a.m.