Simply run the scripts in their numbered order in /scripts
Install necessary packages when required.
If you wish to estimate transcription factor activites and pathway activities with your own RNA data check out our tools :
https://github.com/saezlab/dorothea (TF activities)
https://github.com/saezlab/progeny (pathway activities)
Copyright (C) 2019
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.