malikyousef / mirdrug

miRDrug

miRDrug: Comprehensive Analysis of the Shared Genes Within miRNA-Drug Pairs Using Grouping, Scoring, and Modeling Approach

Emma Qumsiyeh1, Burcu Bakir-Gungor2, and Malik Yousef3,4

1Department of Computer Science and Information Technology, Al-Quds University, Palestine 2Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Turkey 3Department of Information Systems, Zefat Academic College, Zefat, Israel 4Galilee Digital Health Research Center, Zefat Academic College, Zefat, Israel

Corresponding authors:

Malik Yousef: [email protected] Emma Qumsiyeh: [email protected]

Knime Workflow

miRDrug tool is a Knime workflow. In order to run the workflow, you need to download Knime and install it in your local machine. This is the link for downloading Knime: https://www.knime.com/downloads
For more information about the Knime platform you might visit https://www.knime.com/software-overview
See this page for information about setting Knime.
Visit this page for instruction in how to prepare the dataset into Knime table format (*.table) using a Knime workflow
Visit this page for instruction in how to upload the Groups file.
Visit this page for the outputs of GediNET.

Running the workflow:

• You need to use the node “MCCV Iterations” in order to specify the number of Monte Carlo Cross Validation (MCCV) iterations, for example 10 or 100.
• You need to configure the node “List Files/Folders” to point it to the folder that has the gene expression dataset in a table format (as described above)
• You might download an example of such data named GDS2545.table
  

The Pseudocode of miRDrug can seen over this file