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:
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:
Or visit the documentation website:
👉 https://monahton.github.io/GencoDymo2/
👉 https://monahton.github.io/GencoDymo2/articles/GencoDymo2_vignette.html
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!
Monah Abou Alezz, PhD – aboualezz.monah@hsr.it.
San Raffaele Telethon Institute for Gene Therapy (SR-TIGET)
IRCCS San Raffaele Scientific Institute, Milan, Italy
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.
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