Commit Graph

393 Commits

Author SHA1 Message Date
13dc6de5c1 Name annotations to go-terms. 2007-07-24 13:34:40 +00:00
1d517d0754 Changed hardcoded absolute path to relative path. 2007-07-24 13:00:29 +00:00
524c90fcf7 Updated to handle new numpy/scipy. 2007-07-24 12:19:13 +00:00
05274b4f0b confidence 2007-07-23 18:07:10 +00:00
939dba20ee first import lpls 2007-07-23 17:35:28 +00:00
54d271b841 go test data 2007-07-23 17:35:04 +00:00
a05d0faa0d Lib updates 2007-07-23 17:33:21 +00:00
7ea87e646a Added DAG plot to gobrowser module and smokers workflow. 2007-07-23 17:02:28 +00:00
155dfada5c iups 2007-07-23 13:25:34 +00:00
9db5991108 2007-07-20 15:48:59 +00:00
98f53d3448 updates 2007-07-20 12:32:54 +00:00
7ee7aa968a Initial import 2007-07-20 09:36:26 +00:00
dd04e28a62 Query fix 2007-07-05 18:49:24 +00:00
850deeec0d Renamed gene identifers to gene_id 2007-07-05 18:40:29 +00:00
75c7c51708 DistanceToSelectionFunction 2007-07-05 18:36:59 +00:00
3f5d45d7af Renamed smalltest workflow to smokers. 2007-07-05 18:24:45 +00:00
fae096afe4 Changed workflow name from smalltest to smokers, because it is heavily based
on the smokers dataset.
2007-07-05 13:20:52 +00:00
a503ffcdf8 Fixed linewidth in selection in scatter plots. 2007-07-05 11:57:21 +00:00
d29013a863 T-test now works, and outputs a histogram as well as t-values and p-values. 2007-07-03 16:25:38 +00:00
99987999db Broke up a too long line. 2007-07-02 09:54:56 +00:00
884804c49a Added a dummy for the t-test function. Will be updated when I have access to my
office computer tomorrow.
2007-06-28 21:48:13 +00:00
b637a5badc Changed /usr/bin/python2.4 to /usr/bin/python, and hope that 2.5 will not have
trouble running the app.
2007-06-28 21:42:18 +00:00
4eaea2fe59 Added empty lists as default values for all_data and all_plots in Options, so
that subclasses of Options will work with the GUI without modifications.
2007-06-28 21:33:09 +00:00
7b20f44fef Added a GO similarity function that does not do anything useful yet. 2007-06-22 15:37:59 +00:00
e5cd8a8077 Started on a function to enhance gene lists by using GO similarities.
Not in a usable state.
2007-06-22 15:37:22 +00:00
68cc583d2c Added common_dimensions(ds) that lists common dimensions between two
datasets.
2007-06-22 15:35:45 +00:00
ff8833a22c Added read functions for the medium and large smokers sets. 2007-06-21 10:28:10 +00:00
d6298a2d99 Ensures that the GO is only loaded once. 2007-06-21 10:26:35 +00:00
ff2c42902f Commented out some log lines that just cluttered the log. 2007-06-21 10:25:17 +00:00
2eb3d71a5d Moved data/smokers-med to data/smokers-medium. 2007-05-16 15:35:25 +00:00
91032d729e Some more smoker data 2007-05-16 11:45:43 +00:00
7bdfdea23b Added -d option to get all identifiers along a single dimension. 2007-05-16 10:30:54 +00:00
c7bfefe358 Fixed resnik distances. 2007-05-15 18:16:07 +00:00
335efe231a go-gene-matrix takes a GO vs. GO distance matrix and a gene-go-mapping file
and makes a gene vs. go distance matrix based on the shortest distances found
between each gene and go term.
2007-05-15 18:15:51 +00:00
1ab558248c Piping information through dataset -i works. Added names of planned features
to the dataset script.
2007-05-09 21:52:59 +00:00
7272eb63d2 Working on a script to query datasets without starting fluents. 2007-05-09 17:41:50 +00:00
ebe7621817 some biocondoctur utilities 2007-05-06 13:51:06 +00:00
f1301be67a go-distance update. 2007-04-26 18:54:34 +00:00
a0faed2614 Forgot some ... 2007-04-24 17:21:40 +00:00
34ae426c86 Added correlation plot and moved colorbar to plots 2007-04-24 17:17:31 +00:00
90bb25eb55 added default mappable to None 2007-04-24 17:16:34 +00:00
31ac569c3e Added colorbar shortcut 2007-04-24 17:04:29 +00:00
fefaffb2e3 go-distance seems to be able to calculate resnik now. Not asserted with
calculations by hand.
2007-04-04 19:08:50 +00:00
28f0f53e8a go-distance script soon calculating resnik distances. 2007-04-03 13:08:48 +00:00
a5c3a1f154 A couple of extra lines of code in a script. 2007-03-27 13:02:22 +00:00
728c334e8a ontology distance script now accumulates annotations correctly. 2007-03-26 23:15:14 +00:00
11eb3306b9 Works a bit better. 2007-03-26 17:18:26 +00:00
947cf8385f Annotations on yeast from Stanford mdb. 2007-03-23 20:51:04 +00:00
0904a59310 Gene ontolgy distance script in C. Will hopefully speed up calculations when
finished.
2007-03-23 13:25:07 +00:00
6f19fe1b4b Resnick distance matrix 2007-03-16 17:05:46 +00:00