Differences between revisions 2 and 4 (spanning 2 versions)

R2 and Cytoscape: Inferring gene targets by graph based integration and analysis of molecular biological data

Piet Molenaar

Academic Medical Center, University of Amsterdam, the Netherlands

Recipe

Cytoscape version: 2.4 - 2.6

Plugins to Load: BiNGO (Piet: provide link), NetMatch (http://baderlab.org/Software/NetMatch)

GUI steps:

Open website: http://hgserver1.amc.nl/cgi-bin/r2/main.cgi
Logon with: un pw -> if problem switch to ppt (Piet: todo provide restricted access logon)
Click Timeseries: a panel provides you with three choices;
Select TableBuilder:
Choose cellline imr
Choose Notch1
tbc

Data Files: Notch timeseries (Piet: refine this)

Presentation:

Webstart: Time permitting

Video: Time permitting

-  ← Revision 2 as of 2008-08-08 13:58:52 →
  Size: 481
  Editor: PietMolenaar
  Comment:
+  ← Revision 4 as of 2008-08-08 14:16:41 →
  Size: 871
  Editor: PietMolenaar
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 8:
-. Open website: 

 1. Logon with: un pw -> if problem switch to ppt

 1. Click
-Line 12:
+Line 9:
-'''__Plugins to Load__''': Network and Attribute I/O, Network Inference, Functional Enrichment
+''__Cytoscape version__'': 2.4 - 2.6
-Line 14:
+Line 11:
-'''__Data Files__''': Use the notch timeseries (Piet: refine this)
+''__Plugins to Load__'': BiNGO (Piet: provide link), NetMatch (http://baderlab.org/Software/NetMatch)



''__GUI steps__'': 

 1. Open website: http://hgserver1.amc.nl/cgi-bin/r2/main.cgi

 1. Logon with: un pw -> if problem switch to ppt (Piet: todo provide restricted access logon)

 1. Click Timeseries: a panel provides you with three choices; 

 1. Select TableBuilder: 

 1. Choose cellline imr

 1. Choose Notch1

 1. tbc





'''__Data Files__''': Notch timeseries (Piet: refine this)



'''__Presentation__''': 



'''__Webstart__''': Time permitting



'''__Video__''': Time permitting

Diff for "R2InferGeneTargetsRecipe"