diff README @ 7:9d9a06b511ff

Uploaded

--- a/README	Tue Feb 12 15:25:32 2013 -0500
+++ b/README	Tue Feb 19 18:16:12 2013 -0500
@@ -9,3 +9,35 @@
 # GO:TermFinder needs dependencies GraphViz and GD graphics libraries 
 sudo apt-get $APT_OPTS install libgraphviz-perl
 sudo apt-get $APT_OPTS install libgd-gd2-perl
+
+
+--- Term Enrichment related ---
+(currently used - heavily tied to mysql / old data model)
+http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/amigo/amigo/cgi-bin/term_enrichment?view=log
+
+(command line version - file based)
+http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/go-db-perl/
+
+http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/go-db-perl/scripts/go-find-enriched-terms.pl?view=log
+
+--- AmiGO related ---
+
+for AmiGO Manual 
+http://wiki.geneontology.org/index.php/AmiGO_Manual:_Visualize
+
+online tool to play around (current version, has R Wrapper ramigo)
+http://amigo.geneontology.org/cgi-bin/amigo/visualize?mode=client
+
+online tool Amigo2
+http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo?mode=visualize
+
+entry point Amigo2
+https://github.com/kltm/amigo/blob/master/perl/bin/visualize
+
+--- workflows ---
+
+gene set + ontology + gene associations =
+
+gene products + background set = (good) + (ambiguous) + (no match, missing)
+
+