 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 |
|
Einar Ryeng
|
1ab558248c
|
Piping information through dataset -i works. Added names of planned features
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
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
|
0904a59310
|
Gene ontolgy distance script in C. Will hopefully speed up calculations when
finished.
|
2007-03-23 13:25:07 +00:00 |
|
Arnar Flatberg
|
6f19fe1b4b
|
Resnick distance matrix
|
2007-03-16 17:05:46 +00:00 |
|
Einar Ryeng
|
0eff457910
|
Added biological process info to the small smokers example, and a README file to
explain the dataset, at least the non-trivial parts.
|
2007-03-15 23:57:35 +00:00 |
|
Einar Ryeng
|
3dc1867be4
|
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)
|
2007-03-15 23:47:24 +00:00 |
|
Einar Ryeng
|
6fe4ff3c59
|
Added scripts folder for small but useful scripts.
|
2007-03-15 12:46:41 +00:00 |
|
Arnar Flatberg
|
b02773b4e6
|
pls loading plot now have correct name
|
2007-03-15 10:38:52 +00:00 |
|
Arnar Flatberg
|
dbe49b366d
|
added import of networkx
|
2007-03-15 10:38:05 +00:00 |
|
Einar Ryeng
|
f6696dfacc
|
Added gobrowser to smalltest workflow.
|
2007-03-14 21:08:56 +00:00 |
|
Einar Ryeng
|
1c48315a0f
|
Added debug output.
|
2007-03-14 17:26:40 +00:00 |
|
Arnar Flatberg
|
438a268b1d
|
Inserted visible header sort
|
2007-03-14 16:34:50 +00:00 |
|
Arnar Flatberg
|
3d2492578e
|
whitespace
|
2007-03-14 16:33:54 +00:00 |
|
Arnar Flatberg
|
3bd21ab089
|
metric support
|
2007-03-14 16:33:16 +00:00 |
|
Arnar Flatberg
|
48047f1395
|
Moved lots of stuff back to sandbox
|
2007-03-14 16:32:49 +00:00 |
|
Arnar Flatberg
|
7f1f639ee7
|
Updates on metric, whitespace
|
2007-03-14 16:31:25 +00:00 |
|
Arnar Flatberg
|
22f6e3284c
|
whitespace
|
2007-03-14 16:30:18 +00:00 |
|
Arnar Flatberg
|
818dc0b2b0
|
added a logger for constructor calls
|
2007-03-14 16:27:23 +00:00 |
|
Arnar Flatberg
|
212da78933
|
correct comp update
|
2007-03-14 16:17:21 +00:00 |
|
Arnar Flatberg
|
00dd3e8d9d
|
added validation on identifiers input
|
2007-03-14 16:06:16 +00:00 |
|
Arnar Flatberg
|
51435d9fdc
|
Fixed dataset type to network
|
2007-03-14 10:27:08 +00:00 |
|
Arnar Flatberg
|
ac447546a2
|
Annotation file for dim: gene_id
|
2007-03-14 10:26:11 +00:00 |
|
Arnar Flatberg
|
a9981779a6
|
network of articles
|
2007-03-14 10:25:35 +00:00 |
|
Arnar Flatberg
|
9cbefb5705
|
in write_ftsv: adjusted so it splits specifically on tab, whitespace allowed in annotations
|
2007-03-14 10:24:49 +00:00 |