# GencoDymo2: Comprehensive Analysis of GENCODE Annotations and Splice Site Motifs [](https://www.repostatus.org/#active) [](https://www.gnu.org/licenses/gpl-3.0) [](https://github.com/monahton) [](https://github.com/monahton/GencoDymo2/issues) [](https://cran.r-project.org/) [](https://monahton.github.io/GencoDymo2/) [](https://doi.org/10.5281/zenodo.15302316) [](https://cran.r-project.org/package=GencoDymo2) [](https://cran.r-project.org/package=GencoDymo2) [](https://monahton.r-universe.dev/) [](https://monahton.r-universe.dev/) [](https://github.com/monahton/GencoDymo2/commits/main) ------------------------------------------------------------------------ ## 📦 Overview **GencoDymo2** is an R package tailored for dynamic extraction, exploration, and comparison of gene annotations from the [GENCODE](https://www.gencodegenes.org) 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](https://cran.r-project.org/package=GencoDymo2): ``` r # Install the stable version from CRAN install.packages("GencoDymo2") ``` Or you can install the **development version** from GitHub for the latest features: ``` r #Install the development version from GitHub install.packages("pak") pak::pkg_install("monahton/GencoDymo2") ``` ``` r # Load the package library(GencoDymo2) ``` ------------------------------------------------------------------------ ## 🚀 Getting Started To get started, view the vignette: ``` r vignette("GencoDymo2") ``` Or visit the documentation website: 👉 👉 ------------------------------------------------------------------------ ## 📁 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: - 📬 Email: - 🤝 Pull requests encouraged! ------------------------------------------------------------------------ ## :writing_hand: Author **Monah Abou Alezz, PhD** – . San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) IRCCS San Raffaele Scientific Institute, Milan, Italy 🌍 [Personal website](https://monahton.github.io) [](https://saythanks.io/to/monahton) [](https://linkedin.com/in/monah-abou-alezz-phd-06a948ba) ------------------------------------------------------------------------ ## 🧪 Related Projects - [GENCODE](https://www.gencodegenes.org) - 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.