lobigenerator.blogg.se - Cytoscape 3.2

CYTOSCAPE 3.2 HOW TO
CYTOSCAPE 3.2 INSTALL
CYTOSCAPE 3.2 MANUAL

once the metanodes are created, we can change their size, color, shapes as other nodes.Run the "Annotate Cluster" with the option "Create Groups for clusters" checked (Control Panel -> Annotation Panel -> Advanced Option -> Create Groups for clusters). to expand a metanode, double-click on it and the individual nodes forming the group will be displayed.Īdd automatic labels using the "Annotate Cluster" feature (in menu -> EnrichmentMap -> Annotate Cluster).double click on the group on the node to collapse it.Right click on the selected nodes and choose the option "group" => "group selected nodes" => name it

CYTOSCAPE 3.2 MANUAL

manual creation of groups and manual collapsing of nodes (1 by 1).

Use cytoscape 3.2.1 or later and latest EnrichmentMap version (built 627 or later)

CYTOSCAPE 3.2 HOW TO

How to collapse group nodes into a single metanode (in order to simplify the map)

more on java folders and set JAVA_HOME environment variable to Java 7 path:.

the recommended enrichmentmap version for Cytoscape 3.2 is the enrichmap version that contains the automatic annotation option (Release 2.1.0 ).

You can use this script to upgrade your cytoscape 2.8 session files: convert_cyto_28_to_3_EM.sh or use the manual procedure described in the Cytoscape 3.1.1 section See instructions here: here if you have an older Snow Leopard 10.6.8 and need to upgrade to java 7

Once you installed java 7,open your terminal window and type "java -version" if the terminal tells you java version "1.6.x_xx", you may type this command "export JAVA_HOME=$(/usr/libexec/java_home -v 1.7)" to run java 7.

CYTOSCAPE 3.2 INSTALL

To install java 7, you don't need to uninstall java 6 first.java7 is installed by default on (recent) Windows machines but not on MAC machines which run java 1.6 by default.It is based from received feedback from and tailored to the need of the OICR Cancer Stem Cell users ( )ĭo not hesitate to contact us if you need any assistance while executing these steps or have issues not reported on this page ( description on our workflow or how to create a maps, please visit these pages :, This page collects tips on how to use EnrichmentMap and Cytoscape based on frequently asked questions and known issues. TIPS ON HOW TO USE ENRICHMENTMAP AND CYTOSCAPE (provided by the bioinformatics service and EnrichmentMap software developpers) How to make a Cytoscape 2.8 file compatible for Cytoscape 3 :.If you have a project done with Cytoscape 2.8 and want to correctly open these files with Cytoscape 3 you can follow this procedure (recommended for experienced users only)(tips created on Sept 23, 2014):.Move label position of nodes (Oct 5, 2014).Create a figure (manual annotation) with an EnrichmentMap in Cytoscape 3.1.1.

Open an existing enrichment map session file (.cys) (Oct 5, 2014).

Modify the node size to be proportional to GSEA NES (normalized enrichment score).How to create a signature gene-set to use with the post-analysis option of enrichmentmap.How to collapse group nodes into a single metanode (in order to simplify the map).TIPS ON HOW TO USE ENRICHMENTMAP AND CYTOSCAPE (provided by the bioinformatics service and EnrichmentMap software developpers).