R Observatory: Metrics for CNVreg version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CNVreg

1.0

CNV-Profile Regression for Copy Number Variants Association Analysis with Penalized Regression

0packages depend

2.1Kdownloads / year

0.0%test coverage

13/13checks pass

Overview

About

Maintained by Shannon T. HollowayFirst published 2025-03-101 releasesCRAN page ↗

Performs copy number variants association analysis with Lasso and Weighted Fusion penalized regression. Creates a "CNV profile curve" to represent an individual’s CNV events across a genomic region so to capture variations in CNV length and dosage. When evaluating association, the CNV profile curve is directly used as a predictor in the regression model, avoiding the need to predefine CNV loci. CNV profile regression estimates CNV effects at each genome position, making the results comparable across different studies. The penalization encourages sparsity in variable selection with a Lasso penalty and encourages effect smoothness between consecutive CNV events with a weighted fusion penalty, where the weight controls the level of smoothing between adjacent CNVs. For more details, see Si (2024) doi:10.1101/2024.11.23.624994.

Install

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

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

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

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-cnvreg

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-CNVreg

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-CNVreg

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

Health

CRAN checks

13OK

Slowest check: 2.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.13

0.0%

Coverage · measured lines

100%

Documentation · exports

7

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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 · 181 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 75%
Return-value docs: 100%
References docs: 0%

Downloads

2.1K

CRAN downloads in the past year

Rank #19,025 · ~6/day · ~179/mo

Releases R versions

Daily download trend is not available in this view yet.

16630 days

57990 days

2.1K1 year

Compare downloads with other packages →

Also on121 r2u17 autocran

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (7)

statsMatrixdoParallel dplyr foreach glmnet tidyr

LinkingTo (0)

none

Suggests (9)

rmarkdown knitr rlang tidyverse markdown kableExtra patchwork ggplot2 withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Shannon T. Holloway

Contributor, Maintainer

Authors (1)

Yaqin Si

Author

Contributors (2)

Shannon T. Holloway

Contributor, Maintainer

Jung-Ying Tzeng

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-03-10
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 20 KB / 1 file
Download size: 886 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CNVreg")

Format

Holloway, S. T., Si, Y., & Tzeng, J. (2025). CNVreg: CNV-Profile Regression for Copy Number Variants Association Analysis with Penalized Regression (Version 1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.CNVreg

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for CNVreg version 1.0 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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