R Observatory: Metrics for GencoDymo2 version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GencoDymo2

1.0.4

Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs

0packages depend

4.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Monah Abou AlezzFirst published 2025-05-154 releasesCRAN page ↗GitHub ↗

A comprehensive suite of helper functions designed to facilitate the analysis of genomic annotations from the 'GENCODE' database https://www.gencodegenes.org/, supporting both human and mouse genomes. This toolkit enables users to extract, filter, and analyze a wide range of annotation features including genes, transcripts, exons, and introns across different 'GENCODE' releases. It provides functionality for cross-version comparisons, allowing researchers to systematically track annotation updates, structural changes, and feature-level differences between releases. In addition, the package can generate high-quality FASTA files containing donor and acceptor splice site motifs, which are formatted for direct input into the 'MaxEntScan' tool (Yeo and Burge, 2004 doi:10.1089/1066527041410418), enabling accurate calculation of splice site strength scores.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("GencoDymo2", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("monahton/GencoDymo2")

Development version from monahton/GencoDymo2. Installs pak first if it is not already available.

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-gencodymo2

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

Health

CRAN checks

13OK

Slowest check: 8.7 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

14

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMEYes · 327 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 58%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

4.6K

CRAN downloads in the past year

Rank #8,747 · ~13/day · ~384/mo

Releases R versions

Daily download trend is not available in this view yet.

18730 days

1.1K90 days

4.6K1 year

Compare downloads with other packages →

Also on99 r2u

Repository

GitHub ↗ monahton/gencodymo2

3Stars

2Forks

0Open issues

0Open PRs

3Releases

80Commits

4Contributors

License GPL-3.0 · 80 commits · Last activity 2026-02-05

Stars over time

2025-07-11 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/monahton/gencodymo2 on 2026-08-16.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (14)

Biostrings BSgenome data.table (>= 1.17.0)dplyr GenomicRangesmethodsplotrix progress RCurl (>= 1.98.1.17)rtracklayer tidyr IRangestoolsutils

LinkingTo (0)

none

Suggests (5)

devtools BSgenome.Hsapiens.UCSC.hg38 knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Monah Abou Alezz

Author, Maintainer, Copyright holder

Authors (1)

Monah Abou Alezz

Author, Maintainer, Copyright holder

Contributors (3)

Roberta Alfieri

Contributor

Silvia Bione

Contributor

Lorenzo Salviati

Contributor

Copyright holders (1)

Monah Abou Alezz

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.4Latest
2026-01-12 · current release · diff ↗
1.0.3
2025-08-21 · diff ↗
1.0.2
2025-07-14 · diff ↗
1.0.1
2025-05-15
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-15
Total releases: 4 / 1 yrs
License: GPL (>= 3) OSI
Download size: 462 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GencoDymo2")

Format

Abou Alezz, M., Alfieri, R., Bione, S., & Salviati, L. (2026). GencoDymo2: Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs (Version 1.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.GencoDymo2

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 GencoDymo2 version 1.0.4 [Data set]. HJJB, LLC. Data release v2026-08-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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