README.md

In GencoDymo2: Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs

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 development version of GencoDymo2 directly from GitHub:

# install.packages("devtools")
devtools::install_github("monahton/GencoDymo2")

Then load it into your R session:

library(GencoDymo2)

🚀 Getting Started

To get started, view the vignette:

vignette("GencoDymo2")

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

📁 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: [e-mail]
• 🤝 Pull requests encouraged!

:writing_hand: Author

Monah Abou Alezz, PhD – [e-mail].

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.

GencoDymo2 documentation built on June 8, 2025, 10:29 a.m.