GencoDymo2: Comprehensive Analysis of GENCODE Annotations and Splice Site Motifs

📦 Overview

GencoDymo2 is an R package tailored for dynamic extraction, exploration, and comparison of gene annotations from the GENCODE database for human and mouse genomes. This tool facilitates:

Automated retrieval of the latest or specific GENCODE releases
Visualization and quantification of annotation changes across versions
Extraction of introns, exons, splice motifs
Generation of splice site FASTA files for tools like MaxEntScan

It bridges bioinformatics workflows and annotation dynamics, enhancing reproducibility and comparative studies in transcriptome and splicing research.

💻 Installation

You can install the stable version of GencoDymo2 from CRAN:

# Install the stable version from CRAN
install.packages("GencoDymo2")

Or you can install the development version from GitHub for the latest features:

#Install the development version from GitHub
install.packages("pak")
# pak::pkg_install("monahton/GencoDymo2")
install.packages("GencoDymo2", repos = c('https://monahton.r-universe.dev', 'https://cloud.r-project.org'))

# Load the package
library(GencoDymo2)

🚀 Getting Started

To get started, view the vignette:

vignette("GencoDymo2")

Or visit the documentation website:
👉 https://monahton.github.io/GencoDymo2/
👉 https://monahton.github.io/GencoDymo2/articles/GencoDymo2_vignette.html

📁 Functions Highlights

Function	Description
`get_latest_release()`	Retrieves the latest available GENCODE release per species
`compare_release()`	compare annotation statistics between releases
`extract_introns()`	Extracts and processes introns from annotation
`assign_splice_sites()`	Assign the donor and acceptor splice sites
`extract_ss_motif()`	Extract splicing motifs for MaxEntScan tool

🛠️ Development & Contributing

GencoDymo2 is actively developed. Contributions and suggestions are welcome!

🔧 Open issues: https://github.com/monahton/GencoDymo2/issues
📬 Email: aboualezz.monah@hsr.it
🤝 Pull requests encouraged!

:writing_hand: Author

Monah Abou Alezz, PhD – aboualezz.monah@hsr.it.

San Raffaele Telethon Institute for Gene Therapy (SR-TIGET)
IRCCS San Raffaele Scientific Institute, Milan, Italy

🌍 Personal website

🧪 Related Projects

GENCODE
MaxEntScan

📣 Acknowledgments

Developed as part of ongoing research on lncRNA splicing and gene annotation evolution.
Special thanks to colleagues at IGM-CNR and collaborators across splicing research projects.