R Observatory: Metrics for RCNA version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

RCNA

1.0Package record

Robust Copy Number Alteration Detection (RCNA)

0packages depend

2.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Matt BradleyCRAN page ↗

Detects copy number alteration events in targeted exon sequencing data for tumor samples without matched normal controls. The advantage of this method is that it can be applied to smaller sequencing panels including evaluations of exon, transcript, gene, or even user specified genetic regions of interest. Functions in the package include steps for GC-content correction, calculation of quantile based normal karyotype ranges, and calculation of feature score. Cutoffs for "normal" quantile and score are user-adjustable.

Install

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

install.packages("RCNA", 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-rcna

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-RCNA

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-RCNA

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.9 min · r-release-macos-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0

READMEYes · 403 wordsVignettesYes · 1 · staticNEWSYes · 100% structured · does not mention 1.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 8
Examples that run: 100%5 run in a plain check
Exported functions with examples: 71%
Documented parameters: 100%
Return-value docs: 71%
Help pages citing references: 0%

Vignettes (1)

Detecting Copy Number Variation on Targeted Exon Sequencing with RCNA HTML

How these are measured

Downloads

2.3K

CRAN downloads in the past year

Rank #21,861 · ~6/day · ~193/mo

Releases R versions

Daily download trend is not available in this view yet.

18030 days

61390 days

2.3K1 year

Compare downloads with other packages →

Also on69 r2u4 autocran

How downloads are counted

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing RCNA adds 17 packages (7 with compiled code, 11 MB of source tarballs). Heaviest: data.table 5.7 MB, timeSeries 1.4 MB, fBasics 917 KB.

Depends (1)

R >= 3.5.0

Imports (7)

doParallelmethodsutilsmodeest data.table foreach R.utils

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown usethis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Matt Bradley

Author, Maintainer since 1.0 (2024)

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0Latest
record
2024-12-03 · current release
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-12-03
Total releases: 1 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 0.7 KB / 1 file
Download size: 60 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("RCNA")

Format

Bradley, M. (2024). RCNA: Robust Copy Number Alteration Detection (RCNA) (Version 1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.RCNA

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 RCNA version 1.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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