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
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ups
2007-07-28 09:18:48 +00:00
Einar Ryeng
5cf34fc03f
Added information content datasets.
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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.
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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:
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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
...
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
...
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
...
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
Arnar Flatberg