R Observatory: Metrics for ruv version 0.9.7.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ruv

0.9.7.2Package record

Detect and Remove Unwanted Variation using Negative Controls

0packages depend

28.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Johann Gagnon-BartschCRAN page ↗Website ↗

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. 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-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). 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: 2.8 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-09-06
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.9.7.2

READMENoVignettesNoNEWSNoCitation fileNoWebsiteYes

Help pages: 34includes a package overview page
Examples that run: 100%7 run in a plain check
Exported functions with examples: 21%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 38%

How these are measured

Downloads

28.2K

CRAN downloads in the past year

Rank #2,193 · ~77/day · ~2.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.9K30 days

8.1K90 days

28.2K1 year

Compare downloads with other packages →

Also on1.2K r2u7.5K conda_forge34 c2d4u

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing ruv adds 18 packages (7 with compiled code, 14 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

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.

How these are counted

Code & Tests

People & History

People (1)

Johann Gagnon-Bartsch

Author, Maintainer since 0.9.4 (2014)

Releases (6)

Pick two releases to compare their code metrics.

0.9.7.2Latest
record
2026-08-31 · current release · diff ↗
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
0.9.7.1
record
2019-08-30 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.9.7
record
2018-03-12 · diff ↗ ·
added 21 exports
collapse.replicates, design.matrix, google_search, projectionplotvariables, replicate.matrix, RUVI, RUVIII, ruv_cancorplot, ruv_ecdf, ruv_hist, ruv_projectionplot, ruv_rankplot, ruv_residuals, ruv_rle, ruv_scree, ruv_shiny, ruv_summary, ruv_svdgridplot, ruv_svdplot, ruv_varianceplot, ruv_volcano
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.9.6
record
2015-07-18 · diff ↗
0.9.5
record
2015-05-20 · diff ↗

Show 3 earlier eventsHide 3 earlier events

R
R 3.2.0 released · 2015-04-16
0.9.4
record
2014-10-24
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-10-24
Total releases: 6 / 12 yrs
License: GPL
Download size: 41 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ruv")

Format

Gagnon-Bartsch, J. (2026). ruv: Detect and Remove Unwanted Variation using Negative Controls (Version 0.9.7.2) [Computer software]. https://doi.org/10.32614/CRAN.package.ruv

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 ruv version 0.9.7.2 [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.

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