This is the Golem shiny package of iDEP. The reason for this repository is to allow for users to locally install a package version of iDEP.
The data can be retrieved from this here.
Once all the data is retrieved then unzip the data into a base folder, then set up
an environment variable name IDEP_DATABASE
How to make environment variable for each OS:
You need devtools(for Windows you also need RTOOLS)
> devtools::install_github("https://github.com/espors/idepGolem")
# OR you can do the following
$ git clone https://github.com/espors/idepGolem.git
$ cd idepGolem
> devtools::install()
You might get the following output but it still works
* DONE (idepGolem)
Warning messages:
1: 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,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
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
For some Linux OS igraph package may not install correctly look at this issue and then retry the above commands.
How to run the app locally in the browser use the following command
> idepGolem::run_app()
Loading required package: shiny
Listening on http://127.0.0.1:7045
Browsing http://127.0.0.1:7045