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rCNV

An R package for detecting copy number variants from SNPs data

https://github.com/piyalkarum/rcnv

Science Score: 39.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.6%) to scientific vocabulary

Keywords

cnv-analysis copy-number-variation cran gene-duplication genetics genomics landscape-genetics r snps
Last synced: 6 months ago · JSON representation

Repository

An R package for detecting copy number variants from SNPs data

Basic Info
Statistics
  • Stars: 6
  • Watchers: 3
  • Forks: 1
  • Open Issues: 0
  • Releases: 4
Topics
cnv-analysis copy-number-variation cran gene-duplication genetics genomics landscape-genetics r snps
Created almost 5 years ago · Last pushed 9 months ago
Metadata Files
Readme Changelog License

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)
```


[![R-CMD-check](https://github.com/piyalkarum/rCNV/workflows/R-CMD-check/badge.svg)](https://github.com/piyalkarum/rCNV/actions)
[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![Codecov test coverage](https://codecov.io/gh/piyalkarum/rCNV/branch/master/graph/badge.svg)](https://app.codecov.io/gh/piyalkarum/rCNV?branch=master)
[![CRAN status](https://www.r-pkg.org/badges/version/rCNV)](https://CRAN.R-project.org/package=rCNV)
[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/rCNV)](https://cran.r-project.org/package=rCNV)


```{r, echo=FALSE}
cat("# rCNV ")
```


# 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  and navigate to Get started where all the functions and usage are explained with ample examples.***

## Installation  

* CRAN link   
```{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 dont 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

Owner

  • Name: Piyal Karunarathne
  • Login: piyalkarum
  • Kind: user
  • Location: Uppsala, Sweden
  • Company: Uppsala University

I am an evolutionary ecologist. I develop statistical models for biodiversity studies.

GitHub Events

Total
  • Release event: 1
  • Watch event: 1
  • Push event: 2
  • Create event: 1
Last Year
  • Release event: 1
  • Watch event: 1
  • Push event: 2
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 203
  • Total Committers: 3
  • Avg Commits per committer: 67.667
  • Development Distribution Score (DDS): 0.138
Past Year
  • Commits: 23
  • Committers: 2
  • Avg Commits per committer: 11.5
  • Development Distribution Score (DDS): 0.043
Top Committers
Name Email Commits
piyalkarum p****l@y****m 175
Piyal Karunarathne p****e@e****e 22
Klaus Schliep k****p@g****m 6
Committer Domains (Top 20 + Academic)
eb203.ebc.uu.se: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 0
  • Average time to close issues: about 1 month
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 4.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • laneatmore (1)
  • wbsimey (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 306 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: rCNV

Detect Copy Number Variants from SNPs Data

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 306 Last month
Rankings
Forks count: 21.9%
Stargazers count: 28.5%
Dependent packages count: 29.8%
Average: 32.9%
Dependent repos count: 35.5%
Downloads: 48.8%
Maintainers (1)
piyalkarumail@yahoo.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.6.0 depends
  • R.utils * imports
  • colorspace * imports
  • data.table * imports
  • graphics * imports
  • qgraph * imports
  • stringr * imports
  • covr * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/check-r-package v1 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
  • r-lib/actions/setup-r-dependencies v1 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v1 composite
  • r-lib/actions/setup-r-dependencies v1 composite