rCNV

1.3.0

Detect Copy Number Variants from SNPs Data

0packages depend

3.2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Piyal KarunarathneFirst published 2022-04-064 releasesCRAN page ↗GitHub ↗

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).

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("rCNV", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("piyalkarum/rCNV")

Development version from piyalkarum/rCNV. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-rcnv

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-rCNV

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-rCNV

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.9 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 205 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 4%
Documented parameters: 100%
Return-value docs: 100%
References docs: 30%

Downloads

3.2K

CRAN downloads in the past year

Rank #12,851 · ~9/day · ~266/mo

Releases R versions

Daily download trend is not available in this view yet.

28530 days

83690 days

3.2K1 year

Compare downloads with other packages →

Also on159 r2u37 autocran

Repository

GitHub ↗ piyalkarum/rcnv

6Stars

1Forks

0Open issues

0Open PRs

4Releases

233Commits

3Contributors

cnv-analysisgeneticsgenomicslandscape-geneticssnpscopy-number-variationcrangene-duplication

License AGPL-3.0 · 233 commits · Last activity 2026-06-04

Stars over time

2024-11-04 · 62026-07-07 · 6

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/piyalkarum/rcnv on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (6)

data.tablegraphicscolorspace R.utils qgraph stringr

LinkingTo (0)

none

Suggests (4)

rmarkdown knitr testthat covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 3,048 (70%)Rd 1,336 (30%)

Code characteristics

Cyclomatic complexity: 3.0 median / 23 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

51 24 exported

Complexity

6.2 avg / 23 max

Call network

51 nodes / 38 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Datasets

Bundled datasets · 2

Name	Class	Rows × Cols	Also ships in
ADtable	data.frame	3,000 × 109	–
alleleINF	data.frame	2,857 × 28	–

People & History

People (4)

Maintainer (1)

Piyal Karunarathne

Author, Maintainer

Authors (4)

Piyal Karunarathne

Author, Maintainer

Pascal Milesi

Author

Klaus Schliep

Author · added in 1.1.0

Qiujie Zhou

Author

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.3.0Latest
2024-09-20 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.0
2023-08-08 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.0
2022-10-26 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.0
2022-04-06
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-04-06
Total releases: 4 / 4 yrs
License: AGPL (>= 3) OSI
Minimum R: ≥ 3.6.0
Bundled data: 1.6 MB / 3 files
Download size: 2.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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