R Observatory: Metrics for GeneCycle version 1.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GeneCycle

1.1.6Package record

Identification of Periodically Expressed Genes

0packages depend

4.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Miika AhdesmakiCRAN page ↗

The GeneCycle package implements the approaches of Wichert et al. (2004) doi:10.1093/bioinformatics/btg364, Ahdesmaki et al. (2005) doi:10.1186/1471-2105-6-117 and Ahdesmaki et al. (2007) DOI:10.1186/1471-2105-8-233 for detecting periodically expressed genes from gene expression time series data.

Install

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

install.packages("GeneCycle", 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-genecycle

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-GeneCycle

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-GeneCycle

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: 1.0 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.6

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 8 (1 internal)
Examples that run: 86%6 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 50%

How these are measured

Downloads

4.8K

CRAN downloads in the past year

Rank #8,238 · ~13/day · ~396/mo

Releases R versions

Daily download trend is not available in this view yet.

52430 days

1.1K90 days

4.8K1 year

Compare downloads with other packages →

Also on95 r2u10 autocran104 c2d4u

How downloads are counted

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing GeneCycle adds 3 packages (1 with compiled code, 118 KB of source tarballs). Heaviest: fdrtool 59 KB, longitudinal 37 KB, corpcor 22 KB.

Depends (4)

R >= 2.7.0MASSlongitudinal fdrtool (>= 1.2.5)

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Miika Ahdesmaki

Author, Maintainer since 1.1.0 (2008)

Konstantinos Fokianos

Author

Korbinian Strimmer

Author · added in 1.1.6

Previously maintained by Korbinian Strimmer (1.0.0 to 1.0.4).

Listed in earlier versions (1)

Korbinian Strimmer.

no longer listed · 1.0.0 to 1.1.5

Releases (12)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.1.6Latest
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2025-04-02 · current release · diff ↗
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R 4.4.0 released · 2024-04-24
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R 4.3.0 released · 2023-04-21
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R 4.2.0 released · 2022-04-22
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R 4.1.0 released · 2021-05-18
1.1.5
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2021-01-05 · diff ↗
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R 4.0.0 released · 2020-04-24
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R 3.6.0 released · 2019-04-26
1.1.4
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2019-04-25 · diff ↗
1.1.3
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2019-04-18 · diff ↗
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R 3.5.0 released · 2018-04-23
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R 3.4.0 released · 2017-04-21
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R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16

Show 23 earlier eventsHide 23 earlier events

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R 3.1.0 released · 2014-04-10
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R 3.0.0 released · 2013-04-03
1.1.2
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2012-04-16 · diff ↗ ·
added 1 export
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R 2.15.0 released · 2012-03-30
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R 2.14.0 released · 2011-10-31
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R 2.13.0 released · 2011-04-13
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R 2.12.0 released · 2010-10-15
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R 2.11.0 released · 2010-04-22
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R 2.10.0 released · 2009-10-26
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R 2.9.0 released · 2009-04-17
1.1.1
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2009-04-14 · diff ↗
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R 2.8.0 released · 2008-10-20
1.1.0
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2008-07-11 · diff ↗
1.0.4
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2008-06-03 · diff ↗
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R 2.7.0 released · 2008-04-22
1.0.3
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2008-02-06 · diff ↗
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R 2.6.0 released · 2007-10-03
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R 2.5.0 released · 2007-04-24
1.0.2
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2007-02-18 · diff ↗
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R 2.4.0 released · 2006-10-03
1.0.1
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2006-09-29 · diff ↗
1.0.0
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2006-08-11
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R 2.3.0 released · 2006-04-24

Package metadata

First published: 2006-08-11
Total releases: 12 / 20 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.7.0
Bundled data: 118 KB / 1 file
Download size: 139 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GeneCycle")

Format

Ahdesmaki, M., Fokianos, K., & Strimmer, K. (2025). GeneCycle: Identification of Periodically Expressed Genes (Version 1.1.6) [Computer software]. https://doi.org/10.32614/CRAN.package.GeneCycle

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 GeneCycle version 1.1.6 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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