R Observatory: Metrics for ioncopy version 2.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ioncopy

2.2.2Package record

Calling Copy Number Alterations in Amplicon Sequencing Data

0packages depend

2.7Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Jan BudcziesCRAN page ↗

Method for the calculation of copy numbers and calling of copy number alterations. The algorithm uses coverage data from amplicon sequencing of a sample cohort as input. The method includes significance assessment, correction for multiple testing and does not depend on normal DNA controls. Budczies (2016 Mar 15) doi:10.18632/oncotarget.7451.

Install

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

install.packages("ioncopy", 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-ioncopy

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-ioncopy

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-ioncopy

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Jan Budczies <jan.budczies@med.uni-heidelberg.de>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Jan",
                      family = "Budczies",
                      role = c("aut", "cre"),
                      email = "jan.budczies@med.uni-heidelberg.de"),
               person(given = "Eva",
                      family = "Romanovsky",
                      role = "aut"))
as necessary.

CRAN check page ↗

Slowest check: 56 s · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2.2

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9includes a package overview page
Examples that run: 25%1 run in a plain check · 3 never run
Exported functions with examples: 43%
Documented parameters: 100%
Return-value docs: 86%
Help pages citing references: 11%

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #17,788 · ~7/day · ~228/mo

Releases R versions

Daily download trend is not available in this view yet.

25630 days

72990 days

2.7K1 year

Compare downloads with other packages →

Also on86 r2u6 autocran32 c2d4u

How downloads are counted

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing ioncopy adds 31 packages (20 with compiled code, 26 MB of source tarballs). Heaviest: bslib 5.6 MB, promises 3.1 MB, sass 2.9 MB.

Depends (0)

none

Imports (2)

shiny zip

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

Datasets

People & History

People (from the free-text Author field) (2)

Jan Budczies

Eva Romanovsky

· added in 2.0

Maintainer since 1.0 (2015)

Releases (6)

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
R
R 4.1.0 released · 2021-05-18
2.2.2Latest
record
2020-08-11 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
2.1.1
record
2018-03-23 · diff ↗
2.1.0
record
2018-03-14 · diff ↗
2.0.1
record
2018-01-16 · diff ↗
2.0
record
2017-12-05 · diff ↗ ·
removed 2 exports
call.amplicons, call.genes

added 6 exports
read.coverages, assess.CNA, call.CNA, heatmap.CNA, summarize.CNA, runIoncopy
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03

Show 2 earlier eventsHide 2 earlier events

1.0
record
2015-08-26
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-08-26
Total releases: 6 / 11 yrs
License: GPL-3 OSI
Bundled data: 75 KB / 1 file
Download size: 253 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ioncopy")

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 ioncopy version 2.2.2 [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.

Report a problem with this page →