R Observatory: Metrics for CLONETv2 version 2.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CLONETv2

2.2.1Package record

Clonality Estimates in Tumor

0packages depend

3.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Yari CianiCRAN page ↗

Analyze data from next-generation sequencing experiments on genomic samples. 'CLONETv2' offers a set of functions to compute allele specific copy number and clonality from segmented data and SNPs position pileup. The package has also calculated the clonality of single nucleotide variants given read counts at mutated positions. The package has been developed at the laboratory of Computational and Functional Oncology, Department of CIBIO, University of Trento (Italy), under the supervision of prof Francesca Demichelis. References: Prandi et al. (2014) doi:10.1186/s13059-014-0439-6; Carreira et al. (2014) doi:10.1126/scitranslmed.3009448; Romanel et al. (2015) doi:10.1126/scitranslmed.aac9511.

Changes in 2.2.1

Set lower bound for corrected CN ratio (this solves issues for homozygous calls in noisy samples).

From NEWS.md in the release

Install

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

install.packages("CLONETv2", 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-clonetv2

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-CLONETv2

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-CLONETv2

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: 2.5 min · r-oldrel-windows-x86_64

Status changes

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 2.2.1

READMENoVignettesNoNEWSYes · 100% structured · mentions 2.2.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 19includes a package overview page
Examples that run: 63%5 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 39%
Documented parameters: 97%
Return-value docs: 39%
Help pages citing references: 5%

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #11,984 · ~9/day · ~279/mo

Releases R versions

Daily download trend is not available in this view yet.

33030 days

90190 days

3.3K1 year

Compare downloads with other packages →

Also on207 r2u15 autocran

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing CLONETv2 adds 23 packages (12 with compiled code, 21 MB of source tarballs). Heaviest: ggplot2 6.0 MB, dbscan 3.8 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.1

Imports (6)

parallelsets ggplot2 ggrepel arules dbscan

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (4)

Yari Ciani

Maintainer since 2.2.1 (2021) · added in 2.2.1

Davide Prandi

Author

Tarcisio Fedrizzi

Contributor

Alessandro Romanel

Contributor

Previously maintained by Davide Prandi (2.0 to 2.1.0).

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2.2.1Latest
record
2021-10-13 · current release · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
2.1.0
record
2019-05-20 · diff ↗
R
R 3.6.0 released · 2019-04-26
2.0
record
2019-04-05
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-04-05
Total releases: 3 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.1
Download size: 2.6 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CLONETv2")

Format

Ciani, Y., Fedrizzi, T., Prandi, D., & Romanel, A. (2021). CLONETv2: Clonality Estimates in Tumor (Version 2.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.CLONETv2

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 CLONETv2 version 2.2.1 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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