CiiiDER Downloads page

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.

• CiiiDER default - 18 Mb
• CiiiDER with Human genome - 944 Mb
• CiiiDER with Mouse genome - 854 Mb

• Separate files

  • CiiiDER.jar standalone - 16 Mb
  • CiiiDER documentation - 4 Mb
  • JASPAR 2020 transcription factor matrices - <1 Mb
  • Jolma et al. 2013 transcription factor matrices - <1 Mb
  • Human Genome "Homo sapiens.GRCh38.94" - 925 Mb
  • Mouse Genome "Mus musculus.GRCm38.94" - 836 Mb

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 CiiiDER.jar (e.g. ~/Downloads/CiiiDER.jar or C:\file\path\CiiiDER.jar). Note that Windows users may also need to upgrade from 32-bit to 64-bit Java.