Detect Copy Number Variants from SNPs Data

Functions in this package will import filtered variant call format (VCF) files of SNPs data and generate data sets to detect copy number variants, visualize them and do downstream analyses with copy number variants(e.g. Environmental association analyses).

rCNV

rCNV: An R package for detecting copy number variants from SNPs data

Piyal Karunarathne, Qiujie Zhou, Klaus Schliep, and Pascal Milesi

rCNV was designed to identify duplicates (CNV) from SNPs data with ease.

For a comprehensive tutorial on the package, go to https://piyalkarum.github.io/rCNV/ and navigate to “Get started” where all the functions and usage are explained with ample examples.

Installation

• CRAN link https://cran.r-project.org/package=rCNV

install.packages("rCNV")

• You can install the development version of rCNV from GitHub with:

    if (!requireNamespace("devtools", quietly = TRUE)) 
        install.packages("devtools") 
    devtools::install_github("piyalkarum/rCNV", build_vignettes = TRUE)

Please don’t forget to cite us if you use the package.

How to cite

• Karunarathne P, Zhou Q, Schliep K, Milesi P. A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: 'rCNV', a versatile r package for paralogue and CNV detection. Mol Ecol Resour. 2023 Jul 29. doi:http://doi.org/10.1111/1755-0998.13843

• Karunarathne, P., Zhou, Q., Schliep, K., & Milesi, P. (2022). A new framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile R package for paralogs and CNVs detection. BioRxiv, 2022.10.14.512217. doi:http://doi.org/10.1101/2022.10.14.512217