R Observatory: Metrics for iTOP version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

iTOP

1.0.2

Inferring the Topology of Omics Data

0packages depend

2.3Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Nanne AbenFirst published 2018-03-223 releasesCRAN page ↗

Infers a topology of relationships between different datasets, such as multi-omics and phenotypic data recorded on the same samples. We based this methodology on the RV coefficient (Robert & Escoufier, 1976, doi:10.2307/2347233), a measure of matrix correlation, which we have extended for partial matrix correlations and binary data (Aben et al., 2018, doi:10.1101/293993).

Install

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

install.packages("iTOP", 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-itop

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-iTOP

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-iTOP

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

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

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

2

Dependencies · direct

Check history

NOTE2026-03-10
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

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

Downloads

2.3K

CRAN downloads in the past year

Rank #18,180 · ~6/day · ~189/mo

Releases R versions

Daily download trend is not available in this view yet.

15730 days

59790 days

2.3K1 year

Compare downloads with other packages →

Also on98 r2u12 autocran

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (2)

Matrixcorpcor

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown NMF pcalg Rgraphviz

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (1)

Nanne Aben

no longer listed · 1.0.0 to 1.0.2

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
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.2Latest
2018-06-13 · current release · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.1
2018-04-04 · diff ↗
1.0.0
2018-03-22
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-03-22
Total releases: 3 / 8 yrs
License: GPL-2 OSI
Download size: 47 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("iTOP")

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 iTOP version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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