Einar Ryeng
a45743c31e
Added main.py that now contains the One & Only Singleton instance of these classes:
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- 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
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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
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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
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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
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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.
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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
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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
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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
Einar Ryeng
1ab558248c
Piping information through dataset -i works. Added names of planned features
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to the dataset script.
2007-05-09 21:52:59 +00:00
Einar Ryeng
7272eb63d2
Working on a script to query datasets without starting fluents.
2007-05-09 17:41:50 +00:00
Arnar Flatberg
ebe7621817
some biocondoctur utilities
2007-05-06 13:51:06 +00:00
Einar Ryeng
f1301be67a
go-distance update.
2007-04-26 18:54:34 +00:00
Arnar Flatberg
a0faed2614
Forgot some ...
2007-04-24 17:21:40 +00:00
Arnar Flatberg
34ae426c86
Added correlation plot and moved colorbar to plots
2007-04-24 17:17:31 +00:00
Arnar Flatberg
90bb25eb55
added default mappable to None
2007-04-24 17:16:34 +00:00
Arnar Flatberg
31ac569c3e
Added colorbar shortcut
2007-04-24 17:04:29 +00:00
Einar Ryeng
fefaffb2e3
go-distance seems to be able to calculate resnik now. Not asserted with
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calculations by hand.
2007-04-04 19:08:50 +00:00
Einar Ryeng
28f0f53e8a
go-distance script soon calculating resnik distances.
2007-04-03 13:08:48 +00:00
Einar Ryeng
a5c3a1f154
A couple of extra lines of code in a script.
2007-03-27 13:02:22 +00:00
Einar Ryeng
728c334e8a
ontology distance script now accumulates annotations correctly.
2007-03-26 23:15:14 +00:00
Einar Ryeng
11eb3306b9
Works a bit better.
2007-03-26 17:18:26 +00:00
Arnar Flatberg
947cf8385f
Annotations on yeast from Stanford mdb.
2007-03-23 20:51:04 +00:00
Einar Ryeng
Arnar Flatberg