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# GencoDymo2: Comprehensive Analysis of GENCODE Annotations and Splice Site Motifs <img src="man/figures/GencoDymo2_logo.png" align="right" height="140"/>

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---

## 📦 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:  
👉 <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](https://monahton.github.io)

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`r badger::badge_custom("follow me on", "LinkedIn", "blue", "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.