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.
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")# Load the package
library(GencoDymo2)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
| 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 |
GencoDymo2 is actively developed. Contributions and suggestions are welcome!
- 🔧 Open issues: https://github.com/monahton/GencoDymo2/issues
- 📬 Email: [email protected]
- 🤝 Pull requests encouraged!
Monah Abou Alezz, PhD – [email protected].
San Raffaele Telethon Institute for Gene Therapy (SR-TIGET)
IRCCS San Raffaele Scientific Institute, Milan, Italy
- GENCODE
- MaxEntScan
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.