R Observatory: Metrics for GencoDymo2 version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GencoDymo2

1.0.4Package record

Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs

0packages depend

4.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Monah Abou AlezzCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 1.0.4

Bug fixes

Added missing global variable declaration to fix dplyr update (PR #04, thanks @DavisVaughan).

From NEWS.md in the release

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. 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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 8.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10

Show 3 earlier changesHide 3 earlier changes

ERROR12 OK, 1 ERROR2026-05-03
OK12 OK2026-04-25
ERROR12 OK, 1 NOTE, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.4

READMEYes · 327 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.4Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 19
Examples that run: 58%11 run in a plain check · 8 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

GencoDymo2_vignette

How these are measured

Downloads

4.9K

CRAN downloads in the past year

Rank #9,894 · ~14/day · ~411/mo

Releases R versions

Daily download trend is not available in this view yet.

39030 days

99490 days

4.9K1 year

Compare downloads with other packages →

Also on67 r2u

How downloads are counted

Repository

monahton/gencodymo2 ↗Account: monahton

3Stars

2Forks

0Open issues

0Open PRs

3Releases

80Commits

4Commit identities

License file reads as GPL-3.0 · 80 commits · Last activity 2026-02-05 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 12
Median days to close, 50 most recently updated closed PRs: 4

Stars over time

2025-07-11 · 32026-07-07 · 3

How these are measured

PracticesBeta

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

Checks run against github.com/monahton/gencodymo2 on 2026-10-11.

Continuous integration (1)

GitHub Actions

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-02-05 · The repository has a site deploy workflow

pkgdown site last built 2026-02-05

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing GencoDymo2 adds 28 packages (15 with compiled code, 25 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, vctrs 1.0 MB. 5 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

People & History

People (4)

Contributor

Contributor

Contributor

Releases (4)

Pick two releases to compare their code metrics.

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

Cite

Cite this package

Run in R for the authors' entry:

citation("GencoDymo2")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.3389/fgene.2020.00488, 10.5281/zenodo.15302316.

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 v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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