DeepsmirUD_web

Source code of the web interface of DeepsmirUD.

How to run

Due to the computation resource limitation of the cloud service, it is highly recommened to run DeepsmirUD_web on your local computer. You could use one of following approaches,

Using Docker (recommended)

docker run --rm jinlongru/deepsmirud_web

# if the default port 3838 is occupied, you could set a new port by adding `-p` option
docker run --rm -p 3838:3838 jinlongru/deepsmirud_web

Then open your browser and visit http://localhost:3838/ to use the DeepsmirUD database.

Run from GitHub

You need to manually install dependent packages in renv.lock file before running the following command.

R -e "shiny::runGitHub('DeepsmirUD_web/app', 'rujinlong', subdir = 'app')"

Run a cloned version

You need to manually install dependent packages in renv.lock file before running the following command.

git clone https://github.com/rujinlong/DeepsmirUD_web.git
R -e "shiny::runApp('DeepsmirUD_web/app')"

Online version

https://rujinlong.shinyapps.io/DeepsmirUD/

Please note that the online version is not stable and may not work properly.

Citation

If you use DeepsmirUD in your research, please cite the following paper:

Sun J, Ru J, Ramos-Mucci L, et al. DeepsmirUD: Prediction of Regulatory Effects on microRNA Expression Mediated by Small Molecules Using Deep Learning. International Journal of Molecular Sciences. 2023;24(3):1878. doi:https://doi.org/10.3390/ijms24031878