ffe1ce6319
Fixed queries
2007-08-22 13:40:33 +00:00
d510e092e3
Added SAM and conditioned enrichment analysis
2007-08-14 16:16:31 +00:00
13b35180ee
Fixed bug in DAG plot color mapping.
2007-08-08 12:24:14 +00:00
4b80baf225
Added information content drag'n'drop to z loadings plot.
2007-08-06 16:20:39 +00:00
3f7215bc35
Factored out a mixin class for IC thresholding.
2007-08-03 12:09:17 +00:00
94f4b276b9
Fixed selection in DAG-plot to work both with and without IC set.
2007-08-02 11:20:30 +00:00
2d419a9862
Added GO-category enrichment analysis
2007-08-02 11:18:48 +00:00
b233e4abc6
Added spin buttons for minimum and maximum information content in DAG plot.
2007-08-02 10:20:33 +00:00
aa4007e208
Improved drag'n'drop of data into scatter plots so that it no longer requires
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matching identifiers along dimensions.
2007-07-30 17:42:48 +00:00
0bc4a6e3f0
Fixed drag'n'drop of datasets to DAG-plots to convert inf/-inf to
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maximum/minimum values of the dataset.
2007-07-30 14:15:23 +00:00
e84a202fbe
Commented out unused functions.
2007-07-30 10:51:58 +00:00
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
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
939dba20ee
first import lpls
2007-07-23 17:35:28 +00:00
7ea87e646a
Added DAG plot to gobrowser module and smokers workflow.
2007-07-23 17:02:28 +00:00
dd04e28a62
Query fix
2007-07-05 18:49:24 +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
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on the smokers dataset.
2007-07-05 13:20:52 +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
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
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.
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Not in a usable state.
2007-06-22 15:37:22 +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
dbe49b366d
added import of networkx
2007-03-15 10:38:05 +00:00
f6696dfacc
Added gobrowser to smalltest workflow.
2007-03-14 21:08:56 +00:00
6cbf6d0689
Initial commit of small example test workflow
2007-03-13 15:24:20 +00:00
ae9a207a71
Added a tag column in the GO browser to help link it to selections.
2007-03-01 19:13:13 +00:00
89636962a7
Added Workflow.get_data_file_name() which returns the full path to a given
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data file, or None if the file does not exist. This is tested in the test
workflow.
2007-02-28 14:56:24 +00:00
a7c60ffe64
added venn diagram test plot
2007-01-31 13:03:27 +00:00
a65d79697f
Added Expand/Collapse menu choices to the GO browser context menu. This is
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particularly useful when searching for GO terms, because the gtk TreeView
widget does not do interactive search in collapsed parts of the tree.
2007-01-21 16:16:37 +00:00
7693f336ba
Added a singleton project in the project module, so that the current project is
...
easily accessible from anywhere in the code. As there is only one project at
any given time this should not be a problem.
The Gene Ontology browser needed this to be able to set the selection without
passing the current project through several constructors.
Added a context menu in the GO browser that allows the user to select all GO
terms in the subgraph that starts on the current node.
2007-01-18 15:45:48 +00:00
c3c6e85044
Added ImagePlot, which displays a dataset as an image.
2007-01-17 13:20:04 +00:00
f612dda72f
Fixed bug in ftsv save and open dialogs. The save dialog now looks as intended.
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Added the possibility to load several datasets at once. Error handling should still
be improved.
2007-01-16 12:28:56 +00:00
58886726d8
Small updates.
2007-01-12 10:50:55 +00:00
ae3aa7e4aa
Create Resnik distances and save them as ftsv.
2007-01-12 00:00:56 +00:00
e4d7f8e5a2
Resnik distances between GO terms work now.
2007-01-11 22:01:31 +00:00
4b1d16ea78
Updated go-workflow.
2007-01-11 18:57:45 +00:00
9274b044b7
Added read_ftsv in dataset.py. This method reads fluents tab separated values
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files and returns a dataset.
2007-01-10 17:35:58 +00:00
060732d980
More persumably non-working stuff.
2007-01-10 15:33:19 +00:00
1e0b99f283
small bugfix
2007-01-09 08:53:28 +00:00
fa047e0171
Committing non-working code that breaks go workflow. ;)
2007-01-08 21:13:22 +00:00
fac9346aad
Added very hackish annotation count reader.
2006-12-15 12:53:27 +00:00
fb77ddb549
Updated GO workflow. Options class test added. Reading the ontology takes too
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long.
2006-10-26 16:51:42 +00:00
0b30aeac6f
Updated GO workflow.
2006-10-22 23:19:54 +00:00
5491f5ce04
GO workflow. Does not work.
2006-10-22 15:31:36 +00:00
375d45e0cc
Updated import statements, and removed the workflows pca_workflow and
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affy_workflow.
2006-10-17 14:42:27 +00:00
c40f9a2947
Added a LineViewPlot in GenerateData
2006-10-17 13:59:31 +00:00
e0ca48d4b3
Changed how the selection list works. CategoryDatasets can be dragged down to
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the selection list, and will then be converted to Selections.
2006-09-08 18:25:03 +00:00
