R Observatory: Metrics for TROM version 1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2019-12-07. Its history is shown below.

Reason: installation issues were not corrected in time. Missing required BioC 3.11 package

Details below reflect version 1.3, its last release before removal.

TROM

1.3

Transcriptome Overlap Measure

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Jingyi Jessica Li4 releasesCRAN page ↗

A new bioinformatic tool for comparing transcriptomes of two biological samples from the same or different species. The mapping is conducted based on the overlap of the associated genes of different samples. More examples and detailed explanations are available in the vignette. For detailed description of the method, please refer to Li, Wei Vivian, Yiling Chen, and Jingyi Jessica Li. "TROM: A testing-based method for finding transcriptomic similarity of biological samples." Statistics in biosciences 9.1 (2017): 105-136 doi:10.1007/s12561-016-9163-y.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/TROM/TROM_1.3.tar.gz"
pkgFile <- "TROM_1.3.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 (1.3) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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: 96%
Return-value docs: 100%
References docs: 100%

Downloads

TROM Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.1.0latticemethods

Imports (7)

AnnotationDbi openxlsx GO.db gtools RColorBrewer gplots topGO

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 (2)

Other (2)

Jingyi Jessica Li

Contributor

Wei Vivian Li

Contributor · added in 1.1

Listed in earlier versions (1)

Wei Li

no longer listed · 1.0

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2019-12-07
installation issues were not corrected in time Missing required BioC 3.11 package
R
R 3.6.0 released · 2019-04-26
1.3
2018-07-02 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.2
2016-10-07 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.1
2015-06-26 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.0
2015-04-07
R
R 3.1.0 released · 2014-04-10

Package metadata

Total releases: 4
License: GPL-2 OSI
Minimum R: ≥ 3.1.0
Bundled data: 0.7 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("TROM")

Format

Li, J. J., & Li, W. V. (n.d.). TROM: Transcriptome Overlap Measure (Version 1.3) [Computer software]. Retrieved August 15, 2026, from https://CRAN.R-project.org/package=TROM

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 TROM version 1.3 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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