R Observatory: Metrics for bexy version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bexy

0.1.3Package record

Visualize and Parse the Output of 'BeXY'

0packages depend

2.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Madleina CaduffCRAN page ↗

Provides functions for summarizing and plotting the output of the command-line tool 'BeXY' (https://bitbucket.org/wegmannlab/bexy), a tool that performs Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data.

Changes in 0.1.3

Changes:

Updated bexy constructor to accept output from latest version of the command-line tool.
Added functions to generate barplot showing the posterior probabilities of the sex karyotypes.
Improved plotCounts() function to work with cases where multiple X- or Y-linked scaffolds exist.

From NEWS.md in the release

Install

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

install.packages("bexy", 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-bexy

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-bexy

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-bexy

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: 1.5 min · r-release-macos-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-17

Show 2 earlier changesHide 2 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.3

READMENoVignettesNoNEWSYes · 100% structured · mentions 0.1.3Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 41 (20 internal)
Examples that run: 100%20 run in a plain check
Exported functions with examples: 95%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 0%

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #19,930 · ~6/day · ~197/mo

Releases R versions

Daily download trend is not available in this view yet.

23230 days

66890 days

2.4K1 year

Compare downloads with other packages →

Also on162 r2u19 autocran

How downloads are counted

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing bexy adds 35 packages (21 with compiled code, 35 MB of source tarballs). Heaviest: bslib 5.6 MB, sp 4.3 MB, Ternary 4.1 MB.

Depends (0)

none

Imports (2)

TeachingDemos Ternary

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 (4)

Madleina Caduff

Author, Maintainer since 0.1.2 (2023)

Daniel Wegmann

Author

Raphael Eckel

Contributor

Christoph Leuenberger

Contributor

Releases (2)

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
0.1.3Latest
record
2024-08-23 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
0.1.2
record
2023-11-29
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-11-29
Total releases: 2 / 3 yrs
License: GPL-2 OSI
Download size: 40 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bexy")

Format

Caduff, M., Eckel, R., Leuenberger, C., & Wegmann, D. (2024). bexy: Visualize and Parse the Output of 'BeXY' (Version 0.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.bexy

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 bexy version 0.1.3 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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