README.Rmd

---
title: "README"
author: "Piyal Karunarathne"
date: "Last updated: `r format(Sys.time(), '%d %B, %Y')`"
output: md_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

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```{r, echo=FALSE}
cat("# rCNV <img src='man/figures/logo.png' align='right' height='139' />")
```


# rCNV: An R package for detecting copy number variants from SNPs data
`r rCNV:::colorize("Piyal Karunarathne, Qiujie Zhou, Klaus Schliep, and Pascal Milesi","dodgerblue")`

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

![](vignettes/dup.plot.parrotfish.png){width=400}

***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>  
```{r,eval=FALSE}
install.packages("rCNV")
```

* You can install the development version of rCNV from [GitHub](https://github.com/) with:
```{r,eval=FALSE}
    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: 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: 10.1101/2022.10.14.512217