R Observatory: Metrics for bbmix version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bbmix

1.0.0Package record

Bayesian Model for Genotyping using RNA-Seq

0packages depend

3.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Elena VigoritoCRAN page ↗

The method models RNA-seq reads using a mixture of 3 beta-binomial distributions to generate posterior probabilities for genotyping bi-allelic single nucleotide polymorphisms. Elena Vigorito, Anne Barton, Costantino Pitzalis, Myles J. Lewis and Chris Wallace (2023) doi:10.1093/bioinformatics/btad393 "BBmix: a Bayesian beta-binomial mixture model for accurate genotyping from RNA-sequencing."

Install

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

install.packages("bbmix", 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-bbmix

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-bbmix

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 7.9 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29
ERROR12 OK, 1 ERROR2026-07-27
OK12 OK2026-04-25

Show 3 earlier changesHide 3 earlier changes

NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMEYes · 1,052 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 7includes a package overview page
Examples that run: 75%3 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 14%

Vignettes (1)

BBmix installation and usage HTML

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #12,124 · ~9/day · ~274/mo

Releases R versions

Daily download trend is not available in this view yet.

29930 days

91090 days

3.3K1 year

Compare downloads with other packages →

Also on376 r2u

How downloads are counted

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing bbmix adds 52 packages (24 with compiled code, 50 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.4.0

Imports (6)

methodsRcpp rstan R.utils data.table rmutil

LinkingTo (5)

BH Rcpp RcppEigen rstan StanHeaders

Suggests (2)

knitr rmarkdown

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)

Elena Vigorito

Author, Maintainer since 1.0.0 (2023)

Chris Wallace

Author

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.0Latest
record
2023-07-06 · current release
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-07-06
Total releases: 1 / 3 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.4.0
Download size: 270 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bbmix")

Format

Vigorito, E., & Wallace, C. (2023). bbmix: Bayesian Model for Genotyping using RNA-Seq (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.bbmix

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 bbmix version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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