R Observatory: Metrics for SIBERG version 2.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SIBERG

2.0.5Package record

Systematic Identification of Bimodally Expressed Genes Using RNAseq Data

0packages depend

2.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Kevin R. CoombesCRAN page ↗Website ↗

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. 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-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). 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: 1.7 min · r-release-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 2.0.5

READMENoVignettesYes · 1 · dynamicNEWSYes · 33% structuredCitation fileNoWebsiteYes

Help pages: 6
Examples that run: 100%6 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 83%

Vignettes (1)

SIBER Vignette PDF

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #10,970 · ~8/day · ~234/mo

Releases R versions

Daily download trend is not available in this view yet.

48330 days

95490 days

2.8K1 year

Compare downloads with other packages →

Also on89 r2u4 autocran46 c2d4u

How downloads are counted

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing SIBERG adds 1 package (1 with compiled code, 2.7 MB of source tarballs). Heaviest: mclust 2.7 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Kevin R. Coombes

Author, Maintainer since 2.0.0 (2017)

Pan Tong

Author

Listed in earlier versions (1)

Coombes

no longer listed · 2.0.4 to 2.0.5

Releases (6)

Pick two releases to compare their code metrics.

2.0.5Latest
record
2026-09-24 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
2.0.4
record
2025-04-08 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
2.0.3
record
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
unarchivedReturned to CRAN
2018-05-18
2.0.2
record
2018-05-18 · diff ↗
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
record
2017-07-12 · diff ↗

Show 2 earlier eventsHide 2 earlier events

2.0.0
record
2017-07-11
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-07-11
Total releases: 6 / 9 yrs
License: Apache License (== 2.0)
Minimum R: ≥ 2.10
Bundled data: 11 KB / 1 file
Download size: 151 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("SIBERG")

Format

Coombes, K. R., & Tong, P. (2026). SIBERG: Systematic Identification of Bimodally Expressed Genes Using RNAseq Data (Version 2.0.5) [Computer software]. https://doi.org/10.32614/CRAN.package.SIBERG

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 SIBERG version 2.0.5 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →