 Einar Ryeng
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524c90fcf7
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Updated to handle new numpy/scipy.
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2007-07-24 12:19:13 +00:00 |
 Arnar Flatberg
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05274b4f0b
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confidence
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2007-07-23 18:07:10 +00:00 |
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Arnar Flatberg
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939dba20ee
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first import lpls
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2007-07-23 17:35:28 +00:00 |
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Arnar Flatberg
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54d271b841
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go test data
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2007-07-23 17:35:04 +00:00 |
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Arnar Flatberg
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a05d0faa0d
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Lib updates
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2007-07-23 17:33:21 +00:00 |
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Einar Ryeng
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7ea87e646a
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Added DAG plot to gobrowser module and smokers workflow.
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2007-07-23 17:02:28 +00:00 |
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Arnar Flatberg
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155dfada5c
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iups
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2007-07-23 13:25:34 +00:00 |
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Arnar Flatberg
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9db5991108
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2007-07-20 15:48:59 +00:00 |
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Arnar Flatberg
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98f53d3448
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updates
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2007-07-20 12:32:54 +00:00 |
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Arnar Flatberg
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7ee7aa968a
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Initial import
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2007-07-20 09:36:26 +00:00 |
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Arnar Flatberg
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dd04e28a62
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Query fix
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2007-07-05 18:49:24 +00:00 |
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Arnar Flatberg
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850deeec0d
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Renamed gene identifers to gene_id
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2007-07-05 18:40:29 +00:00 |
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Einar Ryeng
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75c7c51708
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DistanceToSelectionFunction
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2007-07-05 18:36:59 +00:00 |
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Einar Ryeng
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3f5d45d7af
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Renamed smalltest workflow to smokers.
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2007-07-05 18:24:45 +00:00 |
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Einar Ryeng
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fae096afe4
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Changed workflow name from smalltest to smokers, because it is heavily based
on the smokers dataset.
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2007-07-05 13:20:52 +00:00 |
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Einar Ryeng
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a503ffcdf8
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Fixed linewidth in selection in scatter plots.
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2007-07-05 11:57:21 +00:00 |
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Einar Ryeng
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d29013a863
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T-test now works, and outputs a histogram as well as t-values and p-values.
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2007-07-03 16:25:38 +00:00 |
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Einar Ryeng
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99987999db
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Broke up a too long line.
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2007-07-02 09:54:56 +00:00 |
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Einar Ryeng
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884804c49a
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Added a dummy for the t-test function. Will be updated when I have access to my
office computer tomorrow.
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2007-06-28 21:48:13 +00:00 |
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Einar Ryeng
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b637a5badc
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Changed /usr/bin/python2.4 to /usr/bin/python, and hope that 2.5 will not have
trouble running the app.
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2007-06-28 21:42:18 +00:00 |
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Einar Ryeng
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4eaea2fe59
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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.
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2007-06-28 21:33:09 +00:00 |
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Einar Ryeng
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7b20f44fef
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Added a GO similarity function that does not do anything useful yet.
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2007-06-22 15:37:59 +00:00 |
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Einar Ryeng
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e5cd8a8077
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Started on a function to enhance gene lists by using GO similarities.
Not in a usable state.
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2007-06-22 15:37:22 +00:00 |
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Einar Ryeng
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68cc583d2c
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Added common_dimensions(ds) that lists common dimensions between two
datasets.
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2007-06-22 15:35:45 +00:00 |
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Einar Ryeng
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ff8833a22c
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Added read functions for the medium and large smokers sets.
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2007-06-21 10:28:10 +00:00 |
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Einar Ryeng
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d6298a2d99
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Ensures that the GO is only loaded once.
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2007-06-21 10:26:35 +00:00 |
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Einar Ryeng
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ff2c42902f
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Commented out some log lines that just cluttered the log.
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2007-06-21 10:25:17 +00:00 |
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Einar Ryeng
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2eb3d71a5d
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Moved data/smokers-med to data/smokers-medium.
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2007-05-16 15:35:25 +00:00 |
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Arnar Flatberg
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91032d729e
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Some more smoker data
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2007-05-16 11:45:43 +00:00 |
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Einar Ryeng
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7bdfdea23b
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Added -d option to get all identifiers along a single dimension.
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2007-05-16 10:30:54 +00:00 |
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Einar Ryeng
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c7bfefe358
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Fixed resnik distances.
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2007-05-15 18:16:07 +00:00 |
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Einar Ryeng
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335efe231a
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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.
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2007-05-15 18:15:51 +00:00 |
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Einar Ryeng
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1ab558248c
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Piping information through dataset -i works. Added names of planned features
to the dataset script.
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2007-05-09 21:52:59 +00:00 |
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Einar Ryeng
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7272eb63d2
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Working on a script to query datasets without starting fluents.
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2007-05-09 17:41:50 +00:00 |
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Arnar Flatberg
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ebe7621817
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some biocondoctur utilities
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2007-05-06 13:51:06 +00:00 |
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Einar Ryeng
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f1301be67a
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go-distance update.
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2007-04-26 18:54:34 +00:00 |
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Arnar Flatberg
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a0faed2614
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Forgot some ...
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2007-04-24 17:21:40 +00:00 |
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Arnar Flatberg
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34ae426c86
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Added correlation plot and moved colorbar to plots
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2007-04-24 17:17:31 +00:00 |
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Arnar Flatberg
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90bb25eb55
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added default mappable to None
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2007-04-24 17:16:34 +00:00 |
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Arnar Flatberg
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31ac569c3e
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Added colorbar shortcut
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2007-04-24 17:04:29 +00:00 |
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Einar Ryeng
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fefaffb2e3
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go-distance seems to be able to calculate resnik now. Not asserted with
calculations by hand.
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2007-04-04 19:08:50 +00:00 |
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Einar Ryeng
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28f0f53e8a
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go-distance script soon calculating resnik distances.
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2007-04-03 13:08:48 +00:00 |
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Einar Ryeng
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a5c3a1f154
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A couple of extra lines of code in a script.
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2007-03-27 13:02:22 +00:00 |
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Einar Ryeng
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728c334e8a
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ontology distance script now accumulates annotations correctly.
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2007-03-26 23:15:14 +00:00 |
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Einar Ryeng
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11eb3306b9
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Works a bit better.
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2007-03-26 17:18:26 +00:00 |
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Arnar Flatberg
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947cf8385f
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Annotations on yeast from Stanford mdb.
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2007-03-23 20:51:04 +00:00 |
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Einar Ryeng
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0904a59310
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Gene ontolgy distance script in C. Will hopefully speed up calculations when
finished.
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2007-03-23 13:25:07 +00:00 |
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Arnar Flatberg
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6f19fe1b4b
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Resnick distance matrix
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2007-03-16 17:05:46 +00:00 |
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Einar Ryeng
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0eff457910
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Added biological process info to the small smokers example, and a README file to
explain the dataset, at least the non-trivial parts.
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2007-03-15 23:57:35 +00:00 |
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Einar Ryeng
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3dc1867be4
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Added entrez-go-mapping that maps entrez IDs to GO terms based on a file of the form:
affy_id ::: geneid_1 /// geneid_2 ::: go(bp) ::: go(cc) ::: go(mf)
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2007-03-15 23:47:24 +00:00 |