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Old 10-22-2013, 09:53 AM   #2
bigmw
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Location: US

Join Date: Aug 2013
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GAGE and Pathview can be used independent of each other. GAGE does pathway and Gene-set Analysis, and works on other tyeps of gene sets than pathways, like GO, coexpressed/coregulated gene sets, TF or miRNA target lists etc. Pathview may integrate and visualizeuser data onto pathway graphs independent of pathway analysis procedure.

Pathview package available at:
http://bioconductor.org/packages/rel.../pathview.html
Here is the info page with example output:
http://pathview.r-forge.r-project.org/
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