Please use the expanding file download navigator below to find the desired files. The best place to start is with a pre-packaged CiiiDER - all of which contain detailed documentation to guide analysis using CiiiDER, JASPAR and Jolma_Cell_2013 transcription factor matrices and the recommended folder structure to get started.
Note that, if there are problems running CiiiDER, particularly with gene names or Ensembl IDs, it may be necessary to increase the memory allocated to Java, so that the genome can be loaded properly.
Please use the Terminal app or Command Prompt (CMD) (depending on whether you have a Mac or Linux machine or are using Windows) to run the CiiiDER JAR file with the following command:
java -Xmx8G -jar CiiiDER.jar
This will launch the normal user interface, but tells Java to run CiiiDER with 8 GB memory. You should also add the file path to
C:\file\path\CiiiDER.jar). Note that Windows users may also need to upgrade from 32-bit to 64-bit Java.