R Observatory: Metrics for polyphemus version 0.3.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2013-07-26. Its history is shown below.

Reason: use of non-portable x11() etc in examples and other issues

Details below reflect version 0.3.4, its last release before removal.

polyphemus

0.3.4

Genome wide analysis of RNA Polymerase II-based ChIP Seq data.

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Martial Sankar1 releasesCRAN page ↗

Polyphemus is able to combine signal intensity (count) profiles, with significant peak annotations in order to identify coding regions of interest for the comparative analysis or two or more samples. The algorithm (i) identifies significant coding regions, (ii) performs normalization, (iii) compares several profiles and (iv) provides matrix output suitable for further clustering analysis.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/polyphemus/polyphemus_0.3.4.tar.gz"
pkgFile <- "polyphemus_0.3.4.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 (0.3.4) 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

6

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 24%

Downloads

polyphemus Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.14.0

Imports (6)

IRanges zoo RUnitparallelR.utils limma

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

People & History

People (3)

Other (3)

Martial Sankar

Contributor

supervised by Marco Mendoza

Contributor

Hinrich Gronenmeyer

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 3.1.0 released · 2014-04-10
archivedRemoved from CRAN
2013-07-26
use of non-portable x11() etc in examples and other issues
R
R 3.0.0 released · 2013-04-03
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
R
R 2.13.0 released · 2011-04-13
R
R 2.12.0 released · 2010-10-15
0.3.4
2010-08-11
R
R 2.11.0 released · 2010-04-22

Package metadata

Total releases: 1
License: GPL (>= 2) OSI
Minimum R: ≥ 2.14.0
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("polyphemus")

Format

Sankar, M., Mendoza, s. b. M., & Gronenmeyer, H. (n.d.). polyphemus: Genome wide analysis of RNA Polymerase II-based ChIP Seq data. (Version 0.3.4) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=polyphemus

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 polyphemus version 0.3.4 [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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