R Observatory: Metrics for ORdensity version 1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2022-12-19. Its history is shown below.

Reason: email to the maintainer was undeliverable

Details below reflect version 1.0, its last release before removal.

ORdensity

1.0

Identification of Differentially Expressed Genes

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by José María Martínez Otzeta1 releasesCRAN page ↗

Automated discovery of differentially expressed genes. The method (called ORdensity) is composed of two phases: discovering potential differentially expressed genes and recognizing differentially expressed genes. It makes use of a permutation resampling procedure to build outlying and density indexes. References: a) Irigoien, I. and Arenas, C. (2018). "Identification of differentially expressed genes by means of outlier detection". doi:10.1186/s12859-018-2318-8. b) Martínez-Otzeta, J. M., Irigoien, I., Sierra, B., and Arenas, C. (2020). "ORdensity: user-friendly R package to identify differentially expressed genes". doi:10.1186/s12859-020-3463-4.

Install

R (source archive)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/ORdensity/ORdensity_1.0.tar.gz"
pkgFile <- "ORdensity_1.0.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-ordensity

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

9

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 14%

Downloads

ORdensity Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on63 r2u

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (9)

clusterdistances Rfast plyrmethodsforeach doRNGparalleldoParallel

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Other (4)

José María Martínez Otzeta

Contributor

Concepción Arenas

Contributor

Basilio Sierra

Contributor

Itziar Irigoien

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2022-12-19
email to the maintainer was undeliverable
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0
2020-05-13
R
R 4.0.0 released · 2020-04-24

Package metadata

Total releases: 1
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Bundled data: 455 KB / 1 file
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ORdensity")

Format

Otzeta, J. M. M., Arenas, C., Sierra, B., & Irigoien, I. (n.d.). ORdensity: Identification of Differentially Expressed Genes (Version 1.0) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=ORdensity

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 ORdensity version 1.0 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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