ComboPred is part of drug combination prediction and testing (DCPT) platform developed by computational systems medicine group at FIMM, University of Helsinki (https://www.fimm.fi/en/research/groups/aittokallio). ComboPred combines the ex vivo sensitivity profiles of the patient’s response to the single compounds, with exome-seq and RNA-seq profiles of the same patient, through a systems-wide compound-target interaction network from our crowdsourcing bioactivity data platform, DrugTargetCommons (DTC) (https://drugtargetcommons.fimm.fi/) to predict combination response. With the predicted combination response, ComboPred calculates combination synergy score with highest single agent (HSA) model.

Data preparation: drug-target interaction matrix, gene expression data for each individual sample, mutation data for each individual sample, drug responses (DSS). Example data can be found in https://github.com/hly89/ComboPred/tree/master/data. And the results are saved csv files.

Run the following command to predict combination response and obtain synergy score and results are save as csv files:

ComboPred (gex, mut, dtm,
                      model.iteration = 6, response, 
                      patient.index = 1, 
                      control.index = 1)

If you have any problems in using ComboPred, please contace Liye He (liye.he@helsinki.fi)

Code released under the MIT license.