Weka implementation of hyperSMURF using EasyEnsemble and SMOTE.
Please read the manual for more information, a detailed installation descriotion and a tutorial.
hyperSMURF requires java 8 and higher. It can be used as a Weka plugin using version 3.9 or higher. To build the program it is recommended to use Maven.
To use hyperSMURF in Weka three steps are needed.
- Clone this repository.
- Compile the java classes and create a Weka plugin using Maven
- Load the plugin into your Weka Package Manager
Use your terminal and go to a folder where you want to checkout hyperSMURF. Then run:
git clone https://github.com/charite/hyperSMURF.git
Go to your repository and create a jar file of hyperSMURF using Maven.
cd hyperSMURF
mvn clean install package
Now you should have the hyperSMURF-0.3.jar in the folder target/. The package phase of Maven creates also the Weka file hyperSMURF-0.3-weka.zip. It is located in the target/ folder.
Open Weka, go to the package manager, and load the file hyperSMURF-0.3-weka.zip into it. Look at the Weka wiki for more information about the Weka Package Manager.
If you want to include hyperSMURF into your java project you can use Maven to download the necessary files from Maven Central. You have to add this code under the dependencies section in your pom.xml:
<dependency>
<groupId>de.charite.compbio</groupId>
<artifactId>hyperSMURF</artifactId>
<version>0.3</version>
</dependency>
Please cite our Scientific Reports article:
M. Schubach, M. Re, P. N. Robinson, and G. Valentini. (2017).
Imbalance-Aware Machine Learning for Predicting Rare and Common Disease-Associated Non-Coding Variants.
Scientific Reports, 7.