comparison README @ 7:9d9a06b511ff

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sudo apt-get $APT_OPTS install libdbi-perl libdbd-mysql-perl

# 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

7:9d9a06b511ff

sudo apt-get $APT_OPTS install libdbi-perl libdbd-mysql-perl

# 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)