If it still does not appear, you likely placed the MCODE.jar file in the wrong directory - this is usually the case if you have multiple versions of Cytoscape installed.It may take up to 30 seconds for the plugin to load up and appear in the menu. Check that MCODE appears in the Plugins menu of Cytoscape.On Unix/Linux or MacOS X, run: cytoscape.sh.This can be done by double-clicking the newly created Cytoscape icon or via commandline: Copy the MCODE.jar file to your /plugins directory. On the rare occasion that it is not, the MCODE and Cytoscape teams will do their best to correct the problem as soon as possible, please be patient and use the previous working versions of Cytoscape and MCODE. In most cases, this version will be compatible with the current Cytoscape version. In such instances, you may check the Show Outdated Plugins check box to display the latest version of MCODE that is available. Otherwise, this may happen when Cytoscape releases an update and MCODE's compatibility information becomes outdated. If you do not see MCODE in this section, it may be because the plugin is already installed and no new versions have come out since the last installation. Go to Available for Install > Analysis and select MCODE. Automated Installation via the Plugin Manager (available with Cytoscape 2.5 or later) Once you have downloaded and installed Cytoscape and verified that it works, MCODE can be installed in two ways. You can download a copy of Cytoscape from. The latest MCODE, version 1.3, requires Cytoscape 2.5.1 or later. The compatible MCODE and Cytoscape versions are outlined in the downloads section on the MCODE website. To use the MCODE plugin, you must first obtain and install Cytoscape.
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