R Observatory: Metrics for ruv version 0.9.7.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CRAN requires the check problems on this package to be fixed before 2026-08-31 or it will be archived.

ruv

0.9.7.1

Detect and Remove Unwanted Variation using Negative Controls

0packages depend

31.8Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Johann Gagnon-BartschFirst published 2014-10-245 releasesCRAN page ↗

Implements the 'RUV' (Remove Unwanted Variation) algorithms. These algorithms attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. These algorithms were proposed in Gagnon-Bartsch and Speed (2012) doi:10.1093/nar/gkz433, Gagnon-Bartsch, Jacob and Speed (2013), and Molania, et. al. (2019) doi:10.1093/nar/gkz433. The algorithms require the user to specify a set of negative control variables, as described in the references. The algorithms included in this package are 'RUV-2', 'RUV-4', 'RUV-inv', 'RUV-rinv', 'RUV-I', and RUV-III', along with various supporting algorithms.

Install

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

install.packages("ruv", 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-ruv

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-ruv

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-ruv

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

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 2.9 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

4

Dependencies · direct

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 38%

Downloads

31.8K

CRAN downloads in the past year

Rank #2,756 · ~87/day · ~2.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.8K30 days

5.8K90 days

31.8K1 year

Compare downloads with other packages →

Also on589 r2u19 autocran5.8K conda_forge14 c2d4u

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

statsggplot2 scales gridExtra

LinkingTo (0)

none

Suggests (2)

shiny colourpicker

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)

Johann Gagnon-Bartsch

no longer listed · 0.9.4 to 0.9.7.1

Package Timeline

5 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
0.9.7.1Latest
2019-08-30 · current release · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.9.7
2018-03-12 · diff ↗
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.9.6
2015-07-18 · diff ↗
0.9.5
2015-05-20 · diff ↗
R
R 3.2.0 released · 2015-04-16

Show 2 earlier events

0.9.4
2014-10-24
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-10-24
Total releases: 5 / 12 yrs
License: GPL
Download size: 42 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ruv")

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 ruv version 0.9.7.1 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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