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559 Commits

Author SHA1 Message Date
Einar Ryeng e84a202fbe Commented out unused functions. 2007-07-30 10:51:58 +00:00
Arnar Flatberg 50a6dae3f6 added full lpls data 2007-07-30 10:21:09 +00:00
Arnar Flatberg b39e71ca2b Trying to fix cv_pls 2007-07-30 09:46:43 +00:00
Einar Ryeng 9ccdf97d07 Changed filenames of information content datasets. 2007-07-30 07:55:36 +00:00
Einar Ryeng 1e18ac81de Added names to datasets. 2007-07-30 07:54:22 +00:00
Arnar Flatberg 349cab3c51 ups 2007-07-28 16:05:11 +00:00
Arnar Flatberg 9a2e259209 c 2007-07-28 09:19:42 +00:00
Arnar Flatberg df88f44255 clean up
ups
2007-07-28 09:18:48 +00:00
Einar Ryeng 5cf34fc03f Added information content datasets.
They are in files named ICs<subgraph><number> where 
those numbered 0 uses all ECs while 5 uses only the safest ones.
2007-07-27 17:22:10 +00:00
Arnar Flatberg 4b8f594966 app -> main.application 2007-07-27 09:40:58 +00:00
Arnar Flatberg 47b89cc411 Fixed bug in esvd for m>n 2007-07-26 18:32:48 +00:00
Arnar Flatberg 7fd4ac6225 pls opt fix 2007-07-26 18:32:27 +00:00
Arnar Flatberg b35f814ef0 Added center check button on lineview 2007-07-26 18:26:50 +00:00
Einar Ryeng dc7f7dbde2 Added existing_identifiers function to Dataset.
Added colouring drag'n'drop to DAGPlot in gobrowser module.
2007-07-26 15:45:42 +00:00
Einar Ryeng a45743c31e Added main.py that now contains the One & Only Singleton instance of these classes:
- Navigator
 - Aplication
 - Workflow
 - Project
 - Options
Corresponding changes have been added in lots of other files to account for this, but
the access to these objects should now be a lot easier.
2007-07-26 12:35:59 +00:00
Arnar Flatberg 91abf12f51 sd 2007-07-24 14:34:47 +00:00
Einar Ryeng 13dc6de5c1 Name annotations to go-terms. 2007-07-24 13:34:40 +00:00
Einar Ryeng 1d517d0754 Changed hardcoded absolute path to relative path. 2007-07-24 13:00:29 +00:00
Einar Ryeng 524c90fcf7 Updated to handle new numpy/scipy. 2007-07-24 12:19:13 +00:00
Arnar Flatberg 05274b4f0b confidence 2007-07-23 18:07:10 +00:00
Arnar Flatberg 939dba20ee first import lpls 2007-07-23 17:35:28 +00:00
Arnar Flatberg 54d271b841 go test data 2007-07-23 17:35:04 +00:00
Arnar Flatberg a05d0faa0d Lib updates 2007-07-23 17:33:21 +00:00
Einar Ryeng 7ea87e646a Added DAG plot to gobrowser module and smokers workflow. 2007-07-23 17:02:28 +00:00
Arnar Flatberg 155dfada5c iups 2007-07-23 13:25:34 +00:00
Arnar Flatberg 9db5991108 2007-07-20 15:48:59 +00:00
Arnar Flatberg 98f53d3448 updates 2007-07-20 12:32:54 +00:00
Arnar Flatberg 7ee7aa968a Initial import 2007-07-20 09:36:26 +00:00
Arnar Flatberg dd04e28a62 Query fix 2007-07-05 18:49:24 +00:00
Arnar Flatberg 850deeec0d Renamed gene identifers to gene_id 2007-07-05 18:40:29 +00:00
Einar Ryeng 75c7c51708 DistanceToSelectionFunction 2007-07-05 18:36:59 +00:00
Einar Ryeng 3f5d45d7af Renamed smalltest workflow to smokers. 2007-07-05 18:24:45 +00:00
Einar Ryeng 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
Einar Ryeng a503ffcdf8 Fixed linewidth in selection in scatter plots. 2007-07-05 11:57:21 +00:00
Einar Ryeng 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
Einar Ryeng 99987999db Broke up a too long line. 2007-07-02 09:54:56 +00:00
Einar Ryeng 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
Einar Ryeng 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
Einar Ryeng 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
Einar Ryeng 7b20f44fef Added a GO similarity function that does not do anything useful yet. 2007-06-22 15:37:59 +00:00
Einar Ryeng 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
Einar Ryeng 68cc583d2c Added common_dimensions(ds) that lists common dimensions between two
datasets.
2007-06-22 15:35:45 +00:00
Einar Ryeng ff8833a22c Added read functions for the medium and large smokers sets. 2007-06-21 10:28:10 +00:00
Einar Ryeng d6298a2d99 Ensures that the GO is only loaded once. 2007-06-21 10:26:35 +00:00
Einar Ryeng ff2c42902f Commented out some log lines that just cluttered the log. 2007-06-21 10:25:17 +00:00
Einar Ryeng 2eb3d71a5d Moved data/smokers-med to data/smokers-medium. 2007-05-16 15:35:25 +00:00
Arnar Flatberg 91032d729e Some more smoker data 2007-05-16 11:45:43 +00:00
Einar Ryeng 7bdfdea23b Added -d option to get all identifiers along a single dimension. 2007-05-16 10:30:54 +00:00
Einar Ryeng c7bfefe358 Fixed resnik distances. 2007-05-15 18:16:07 +00:00
Einar Ryeng 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