R Observatory: Metrics for SIBERG version 2.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SIBERG

2.0.4

Systematic Identification of Bimodally Expressed Genes Using RNAseq Data

0packages depend

2.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Kevin R. CoombesFirst published 2017-07-115 releasesCRAN page ↗

Provides models to identify bimodally expressed genes from RNAseq data based on the Bimodality Index. SIBERG models the RNAseq data in the finite mixture modeling framework and incorporates mechanisms for dealing with RNAseq normalization. Three types of mixture models are implemented, namely, the mixture of log normal, negative binomial, or generalized Poisson distribution. See Tong et al. (2013) doi:10.1093/bioinformatics/bts713.

Install

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

install.packages("SIBERG", 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-siberg

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

# 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-SIBERG

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-SIBERG

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 1.2 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

1

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 83%

Downloads

2.5K

CRAN downloads in the past year

Rank #17,415 · ~7/day · ~206/mo

Releases R versions

Daily download trend is not available in this view yet.

17830 days

63790 days

2.5K1 year

Compare downloads with other packages →

Also on103 r2u25 autocran26 c2d4u

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (1)

mclust

LinkingTo (0)

none

Suggests (2)

edgeR doParallel

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Kevin R. Coombes

Author, Maintainer

Authors (2)

Kevin R. Coombes

Author, Maintainer

Pan Tong

Author

Listed in earlier versions (1)

Coombes

no longer listed · 2.0.4

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
2.0.4Latest
2025-04-08 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
2.0.3
2022-05-03 · diff ↗
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
R
R 3.6.0 released · 2019-04-26
2.0.2
2018-05-18 · diff ↗
unarchivedReturned to CRAN
2018-05-18
R
R 3.5.0 released · 2018-04-23
archivedRemoved from CRAN
2018-02-20
check problems were not corrected despite reminders Unconditional use of Suggests package(s) from BioC
2.0.1
2017-07-12 · diff ↗
2.0.0
2017-07-11

Show 1 earlier events

R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-07-11
Total releases: 5 / 9 yrs
License: Apache License (== 2.0)
Minimum R: ≥ 2.10
Bundled data: 11 KB / 1 file
Download size: 152 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SIBERG")

Format

Coombes, K. R., & Tong, P. (2025). SIBERG: Systematic Identification of Bimodally Expressed Genes Using RNAseq Data (Version 2.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.SIBERG

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 SIBERG version 2.0.4 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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