iDEP is a bioinformatics platform for analyzing gene expression data graphically, interactively, and reproducibly. The input file is a gene-level expression matrix derived from RNA-Seq, microarray, proteomics, or other methods. Hosted at South Dakota State Univerisity, iDEP is developed as an R package based on the Golem framework, by a small team led by Dr. Steven Ge. See documentation and paper.
(CC BY-NC 3.0) Non-commercial use. For local installation at private institutions, please contact us.
Following the redesign of our database, the updated iDEP can now be effortlessly executed on a laptop or local server. Please be aware that iDEP undergoes frequent updates; if you are running the software locally, we recommend updating to the most recent version on a monthly basis.
Once installed as an R package, iDEP can be initiated from R using the iDEP::run_app()
command. However, this approach can be time-consuming, as it necessitates the installation of all 355 dependent R packages. This process takes approximately an hour on Windows 10, and potentially even longer for Mac or Linux users due to potential troubleshooting requirements for many of the R packages.
A more efficient alternative is to utilize the iDEP Docker image available on DockerHub. The only prerequisite is to install the Docker software on Linux or Docker Desktop on Windows or MacOS.
Please note that local installation is free for non-profit organizations only.
Most of modern laptop can run iDEP locally, if it has more than 10GB storage and 4GB of memory.
Just follow this detailed video. No prior experience with Docker is needed.
docker run --pull always -d --name idep -p 3838:3838 gexijin/idep:latest
Note that the Docker engine is now running in the backgroup, acting as a webserver. It works even if you restart your computer. To stop it, run these from Windows PowerShell:
docker stop idep
docker rm idep
After stopping it, you can restart it by repeating Step 5, which also pulls the latest Docker image from DockerHub. Make sure you update your image at least on a monthly basis.
install.packages("devtools")
devtools::install_github("https://github.com/gexijin/idepGolem", upgrade = "never")
You might get the following warnings, which can be ignored.
WARNING: Rtools is required to build R packages, but is not currently installed.
package ‘KEGG.db’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
2: In i.p(...) : installation of package ‘GO.db’ had non-zero exit status
3: In i.p(...) :
installation of package ‘/tmp/RtmpCpiUsZ/file2326c2a50656f/PGSEA_1.60.0.tar.gz’ had non-zero exit status
idepGolem::run_app()
The benefit of this approach is that you always have the most recent version from GitHub. The next time you install iDEP, it will take much less time as the dependencies have been installed.
With this method, users can customize iDEP by changing the source code. We also welcome contributions through Pull Requests on GitHub.
install.packages("golem")
install.packages("devtools")
devtools::install_github("https://github.com/gexijin/idepGolem", upgrade = "never")
remove.packages("idepGolem")
run_dev.R
script. If some R packages are missing, install them and try again. Note that the app is devided into 11 Shiny Modules.See video for more details. No prior experience with Docker is needed.
terminal
in the search field. Then click the Terminal app. docker run --pull always -d --name idep -p 3838:3838 gexijin/idep:latest
Note that the Docker engine is now running in the backgroup, acting as a webserver. It works even if you restart your computer. To stop it, run these from the Terminal app:
docker stop idep
docker rm idep
After stopping it, you can restart it by repeating Step 4, which also pulls the latest Docker image from DockerHub. Make sure you upgrade your iDEP image at least on a monthly basis.
Alternatively, you can also install iDEP as an R package or copy the iDEP code locally. The method is the same as above in the Windows section.
curl -fsSL https://get.docker.com -o install_docker.sh
sudo sh install_docker.sh
sudo docker run --pull always -d --name idep -p 3838:3838 gexijin/idep:latest
Note that the Docker engine is now running in the backgroup, acting as a webserver. To stop it:
sudo docker stop idep
sudo docker rm idep
After stopping it, you can restart it by repeating Step 2, which also pulls the latest iDEP image from DockerHub. We update it frequently, make sure you upgrade your image at least on a monthly basis.