CLONETv2

2.2.1

Clonality Estimates in Tumor

0packages depend

3.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Yari CianiFirst published 2019-04-053 releasesCRAN 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.

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.

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).

Health

CRAN checks

13OK

Slowest check: 3.0 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

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 63%
Documented parameters: 97%
Return-value docs: 39%
References docs: 5%

Downloads

3.3K

CRAN downloads in the past year

Rank #12,675 · ~9/day · ~272/mo

Releases R versions

Daily download trend is not available in this view yet.

27930 days

84590 days

3.3K1 year

Compare downloads with other packages →

Also on246 r2u36 autocran

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

R 1,855 (69%)Rd 841 (31%)

Code characteristics

Cyclomatic complexity: 3.0 median / 20 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

32 7 exported

Complexity

4.9 avg / 20 max

Call network

32 nodes / 32 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

People & History

People (4)

Maintainer (1)

Yari Ciani

Maintainer · added in 2.2.1

Authors (1)

Davide Prandi

Author

Contributors (2)

Tarcisio Fedrizzi

Contributor

Alessandro Romanel

Contributor

Package Timeline

3 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
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
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
2019-05-20 · diff ↗
R
R 3.6.0 released · 2019-04-26
2.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

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