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Usage
Helps to use HiTS
Featured UsageAfter you have installed all dependencies and the HiTS plugins you are almost ready to use this program. (We are assuming you have set the proxy settings if you need them in one of the previous steps.) Additional preparationsIf you want to use the CellHTS2, or biomaRt Annotator node, you have to start Rserve. Starting KNIMEWhen you are analysing large experiments your default memory size set for KNIME may be not enough. In that case you should increase the memory, by changing the line starting with -Xmx in your knime.ini file. -Xmx1024M is not a bad choice if your computer has enough physical memory installed. You might want to add -Dknime.expert.mode=true to your knime.ini file. This will allow you to use the Dendrogram with Heatmap node, and the looping support of KNIME. It also allows you to select custom normalisation/scoring methods too. After this you can start your KNIME installation. Configure your preferencesAfter you have started KNIME you should see (in your default KNIME perspective) the HiTS nodes in the Node Repository. You can customise your preferences in the File/Preferences... menu. There you can find KNIME/HiTS Preferences. On that page you have several options:
The usage of the nodes is similar to the other KNIME nodes. You can get more help on their Node Description views, or the wiki pages listed below:
Common use casesThis page shows some usecases of the program with KNIME. Try itYou can find workflows in this folder's subfolders if you want to try this without problems. For sample data check this folder. Sample data created with Amanda Birmingham's NoiseMaker program. Reporting Bugs, Request FeaturesIf you encounter a bug, please report it at this page. It is also for feature requests. Please be so kind if you see the same request or bug there then just star it. Thank you. |