The objective of this repository is to share the code to reproduce all the analyses described in the following article:
Functional networks of co-expressed genes to explore iron homeostasis processes in the pathogenic yeast Candida glabrata - Denecker et al
To reproduce the analyses, we provide a docker image with Rstudio and all the necessary packages installed : https://cloud.docker.com/repository/docker/tdenecker/ihkg/general
It is possible to find the complete source code for iHKG viewer hosted at the following address : https://thomasdenecker.github.io/iHKG/
We use Docker to develop and run iHKG Rstudio. We invite you to ensure you have installed the following requirements before trying to bootstrap the application:
We recommend you to follow Docker's official documentations to install required docker tools (see links above).
Docker must be on for the duration of iHKG Rstudio use.
Did you read the "Requirements" section above?
Download the zip file (here), extract this file and copy the obtained folder where you want on your computer. Note that if you move the folder, the installation procedure will have to be redone.
Reminder : Docker must always be switched on for any installation and use of iHKG code !
IMPORTANT : iHKG project needs Docker. It will only be possible to install on Windows 10.
In this folder, you will find a file named INSTALLATION_WINDOWS.bat. By double clicking on it, the installation will begin. This may take a little time depending on the quality of your internet connection. When the installation is completed, a new file will appear. They allow to launch the iHKG Rstudio.
In command line
Open a terminal and run these commands:
git clone https://github.com/thomasdenecker/iHKG.git
cd iHKG
sudo ./INSTALLATION_MAC.sh
The installation will begin. This may take a little time depending on the quality of your internet connection. When the installation is completed, a new file will appear. They allow to launch the iHKG Rstudio. Once the installation is complete, use this command to launch iHKG Rstudio:
./iHKG.sh
NOTE
You can also double click the file iHKG.sh . In this situation a small manipulation is required (only once). In the Finder, right-click the file iHKG.sh and select "Open with" and then "Other...".
You can select the application you want the file to be execute with. In this case it should be the Terminal. To be able to select the Terminal, you have to switch from "Recommended Applications" to "All Applications" (the Terminal.app application can be found in the Utilities folder).
Check "Always Open With" and after clicking OK you should be able to execute you SHELL script by simply double-clicking it.
In command line
Open a terminal and run these commands:
git clone https://github.com/thomasdenecker/iHKG.git
cd iHKG
sudo ./INSTALLATION_LINUX.sh
The installation will begin. This may take a little time depending on the quality of your internet connection. When the installation is completed, a new file will appear. They allow to launch the iHKG Rstudio. Once the installation is complete, use this command to launch iHKG Rstudio:
sudo ./iHKG.sh
Double click on iHKG file (Windows / MacOS X) or launch the command line (Linux / MacOS X) and open your internet browser, typing the following url: http://localhost:8788/ and it should work.
NOTE (MAC users) : You may need to repeat the same manipulation as for the installation file (only once).
If you use iHKG project, please cite our paper :
Functional networks of co-expressed genes to explore iron homeostasis processes in the pathogenic yeast Candida glabrata - Denecker et al
Please, see the CONTRIBUTING file.
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms. See CODE_OF_CONDUCT file.
iHKG is released under the BSD-3 License. See the bundled LICENSE file for details.