|
38
|
1 Welcome to OBO Tools
|
|
0
|
2 The following libraries need to be installed to use the obo tools:
|
|
|
3
|
|
|
4 # termfinder needs g++ and other build tools
|
|
|
5 sudo apt-get $APT_OPTS install build-essential
|
|
|
6
|
|
|
7 # perl dbi / perl DBD::mysql
|
|
|
8 sudo apt-get $APT_OPTS install libdbi-perl libdbd-mysql-perl
|
|
|
9
|
|
|
10 # GO:TermFinder needs dependencies GraphViz and GD graphics libraries
|
|
|
11 sudo apt-get $APT_OPTS install libgraphviz-perl
|
|
|
12 sudo apt-get $APT_OPTS install libgd-gd2-perl
|
|
7
|
13
|
|
|
14
|
|
|
15 --- Term Enrichment related ---
|
|
|
16 (currently used - heavily tied to mysql / old data model)
|
|
|
17 http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/amigo/amigo/cgi-bin/term_enrichment?view=log
|
|
|
18
|
|
|
19 (command line version - file based)
|
|
|
20 http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/go-db-perl/
|
|
|
21
|
|
|
22 http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/go-db-perl/scripts/go-find-enriched-terms.pl?view=log
|
|
|
23
|
|
8
|
24 --- Gene Associations ---
|
|
|
25 svn --ignore-externals co svn://ext.geneontology.org/trunk/gene-associations gene-associations
|
|
|
26
|
|
7
|
27 --- AmiGO related ---
|
|
|
28
|
|
|
29 for AmiGO Manual
|
|
|
30 http://wiki.geneontology.org/index.php/AmiGO_Manual:_Visualize
|
|
|
31
|
|
|
32 online tool to play around (current version, has R Wrapper ramigo)
|
|
|
33 http://amigo.geneontology.org/cgi-bin/amigo/visualize?mode=client
|
|
|
34
|
|
|
35 online tool Amigo2
|
|
|
36 http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo?mode=visualize
|
|
|
37
|
|
|
38 entry point Amigo2
|
|
|
39 https://github.com/kltm/amigo/blob/master/perl/bin/visualize
|
|
|
40
|
|
|
41 --- workflows ---
|
|
|
42
|
|
|
43 gene set + ontology + gene associations =
|
|
|
44
|
|
|
45 gene products + background set = (good) + (ambiguous) + (no match, missing)
|
|
|
46
|
|
|
47
|
