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  • 7600abf372 Deleted all datasets. They don't belong here. einarr 2007-12-12 17:02:28 +00:00
  • 05cf63e694 Removes rpy, forcing scipy to be used. einarr 2007-12-12 14:41:27 +00:00
  • 455b2a7a86 Small fixes to setup.py and rules. einarr 2007-12-11 19:49:36 +00:00
  • 1798279a32 Files to debianize the program. einarr 2007-12-11 18:26:47 +00:00
  • 6379acca58 Added setup.py to do installation. einarr 2007-12-11 18:25:08 +00:00
  • cef882b0a4 * Annotations are no longer cluttered as if they all belong to the same dimension. There was a bug that actually gave the same annotation dictionary to all dictionary annotation handlers. * The selection window now remembers which annotation was shown for each dimension. einarr 2007-12-11 13:47:29 +00:00
  • c862c8bb04 Added function to specify a specific workflow based on module name. einarr 2007-12-11 11:40:27 +00:00
  • 9242b88d07 Removed buttons that do not belong on the toolbar: "New", "Load", "Save". Load and save are currently not implemented anyway, but they do not represent frequently used actions anyway. einarr 2007-12-11 10:13:31 +00:00
  • 90c84b768a Changed help URLs. einarr 2007-12-11 01:11:13 +00:00
  • 057e2a9f1d About to change the way logging is normally called. einarr 2007-12-11 01:02:47 +00:00
  • d0a7b1cbc2 Code cleanup. einarr 2007-12-11 00:13:26 +00:00
  • 055c0ea4ac Dataset dimensions are shown in statusbar. einarr 2007-12-10 21:08:09 +00:00
  • 1a4d73f26b Fixed the function menu. It now works, is placed before "Help", and the method for running a function is moved to the workflow module instead of being hidden the WorkflowView. einarr 2007-12-10 16:57:38 +00:00
  • 82dacc3dd1 Added menu items to toggle visibility of workflow, navigator and infopane. einarr 2007-12-06 00:20:42 +00:00
  • 27d935319c Added a delete function to the context menu on navigator elements. einarr 2007-11-09 15:02:32 +00:00
  • c26999e688 Added line plot of matrices. einarr 2007-11-08 11:47:36 +00:00
  • 7ee7f0cf7e Added scatter plotting from dataset in navigator. einarr 2007-11-07 12:44:22 +00:00
  • aef2e1daf0 Tralala ... flatberg 2007-11-07 12:34:13 +00:00
  • ca51a0b382 Added mat2ftsv to naïvely convert matlab matrices to ftsv files. Works in at least one case, but does not try to guess anything sensible for identifiers. einarr 2007-10-31 17:43:02 +00:00
  • b114d5aeec New crossval index generator flatberg 2007-09-25 06:31:40 +00:00
  • 18f33decc7 Finnished the l-pls fdr flatberg 2007-09-21 13:16:40 +00:00
  • 6698ebe932 Removed actiavtion in dimcontroller opt. of compare func flatberg 2007-09-20 16:12:58 +00:00
  • 41f93c5989 .... flatberg 2007-09-20 16:11:37 +00:00
  • 7e9a0882f1 Updates flatberg 2007-09-20 16:10:40 +00:00
  • 7ef01d37f0 tasks flatberg 2007-09-03 17:51:22 +00:00
  • 5a1e225a08 working test ... for real flatberg 2007-09-03 16:16:39 +00:00
  • 9a296f59f6 bugfix on scipy import flatberg 2007-09-03 16:16:05 +00:00
  • f8e0cfdb8b removed unused workflows flatberg 2007-09-03 15:50:16 +00:00
  • 2fdd9aaf77 initial working test wf flatberg 2007-09-03 15:46:45 +00:00
  • bfb039328c Some stuff on tasks. einarr 2007-09-03 13:22:11 +00:00
  • d9e5398865 GO (id, description, definition, ontology) flatberg 2007-08-28 09:39:24 +00:00
  • 16ed2fd9c9 u flatberg 2007-08-24 11:48:29 +00:00
  • dc43830752 HS-entrez annotations flatberg 2007-08-24 09:15:16 +00:00
  • 7dbf28f65d ... just lots of stuff flatberg 2007-08-24 09:14:24 +00:00
  • 21b63b17e5 Fixed axis bug in barplot flatberg 2007-08-24 09:13:34 +00:00
  • 7538710144 Enabled tree lines and set sensitivity on transforms flatberg 2007-08-24 09:12:52 +00:00
  • fa4604dbe5 load dataset defaults to datadir flatberg 2007-08-22 14:05:51 +00:00
  • 01ef4bdedd Added support for identifiers sorting, and selection flatberg 2007-08-22 13:41:04 +00:00
  • ffe1ce6319 Fixed queries flatberg 2007-08-22 13:40:33 +00:00
  • 6ba8c6eb67 ups flatberg 2007-08-21 10:31:09 +00:00
  • e06eeb6d17 ups flatberg 2007-08-21 10:25:23 +00:00
  • 26ab6c3fe7 Added a "decimals" parameter to write_ftsv, so that datasets can be written without full precision. Defaults to 7 digits after decimal point. einarr 2007-08-16 10:02:54 +00:00
  • a6af506ae0 The reduced Uma X, for use in Lpls flatberg 2007-08-16 09:46:33 +00:00
  • fc91d17bdc The Uma affy, nci60 + drug data + tissue type flatberg 2007-08-16 09:17:07 +00:00
  • d510e092e3 Added SAM and conditioned enrichment analysis flatberg 2007-08-14 16:16:31 +00:00
  • 8d4848d5fa Added explained variance flatberg 2007-08-14 16:12:28 +00:00
  • 004cfe0a9f Quick fix for gray on NaNs flatberg 2007-08-14 16:10:35 +00:00
  • 13b35180ee Fixed bug in DAG plot color mapping. einarr 2007-08-08 12:24:14 +00:00
  • e08dba0924 read_ftsv and write_ftsv now supports filenames as well as file descriptors. einarr 2007-08-08 12:23:45 +00:00
  • 04126e9c83 New information content datasets. einarr 2007-08-08 10:13:05 +00:00
  • 46c2a0c149 New calculations (Z), based on updated X data flatberg 2007-08-07 11:45:16 +00:00
  • 916fc4c046 Added scaling to navigator menu, moved transformations to a separate sub menu flatberg 2007-08-07 11:42:07 +00:00
  • 168384f266 Cleaned esvd routine, added subfunc scale flatberg 2007-08-07 11:41:03 +00:00
  • d055a1f882 Some ..... flatberg 2007-08-07 11:39:16 +00:00
  • 4b80baf225 Added information content drag'n'drop to z loadings plot. einarr 2007-08-06 16:20:39 +00:00
  • 72e300c95e Addded automatic bin selection in histogram plot flatberg 2007-08-04 10:37:22 +00:00
  • 3f7215bc35 Factored out a mixin class for IC thresholding. einarr 2007-08-03 12:09:17 +00:00
  • 0523ebab05 Added dataset transpose option flatberg 2007-08-03 09:44:31 +00:00
  • e62a6ae9b3 Removed print statements flatberg 2007-08-02 14:51:53 +00:00
  • 0758ab8bfb Fixed histogram plot to accept selections of one, and made ad-hoc choice of proportional color to patches flatberg 2007-08-02 14:37:19 +00:00
  • 7a0e2481eb Full corrected X data flatberg 2007-08-02 11:22:05 +00:00
  • 94f4b276b9 Fixed selection in DAG-plot to work both with and without IC set. einarr 2007-08-02 11:20:30 +00:00
  • b334e94b15 New and corrected smokers data flatberg 2007-08-02 11:19:47 +00:00
  • 438e7cb918 Irrelevant play flatberg 2007-08-02 11:19:16 +00:00
  • 2d419a9862 Added GO-category enrichment analysis flatberg 2007-08-02 11:18:48 +00:00
  • 973470b595 stuff flatberg 2007-08-02 11:18:18 +00:00
  • da5b977042 Moved less important datasets into a subfolder named "secondary". einarr 2007-08-02 10:52:58 +00:00
  • 83d76eac4f Fixed vorrect namespace for scipy funcs flatberg 2007-08-02 10:44:06 +00:00
  • b233e4abc6 Added spin buttons for minimum and maximum information content in DAG plot. einarr 2007-08-02 10:20:33 +00:00
  • dc3893eecc Fixed a "main.project" bug flatberg 2007-08-02 10:19:16 +00:00
  • f12fe23c1b Fixed docstrings. einarr 2007-08-02 10:08:52 +00:00
  • 4c24061575 Fixed docstrings. einarr 2007-08-02 10:08:27 +00:00
  • 63d6347f37 Fixed makefile to not use lots of space on inherited function documentation. einarr 2007-08-02 10:04:06 +00:00
  • 6e4db7ebe4 Fixed plot focus signal problem. einarr 2007-07-31 12:25:56 +00:00
  • 10eba079bc iii flatberg 2007-07-30 18:04:42 +00:00
  • aa4007e208 Improved drag'n'drop of data into scatter plots so that it no longer requires matching identifiers along dimensions. einarr 2007-07-30 17:42:48 +00:00
  • 0bc4a6e3f0 Fixed drag'n'drop of datasets to DAG-plots to convert inf/-inf to maximum/minimum values of the dataset. einarr 2007-07-30 14:15:23 +00:00
  • e84a202fbe Commented out unused functions. einarr 2007-07-30 10:51:58 +00:00
  • 50a6dae3f6 added full lpls data flatberg 2007-07-30 10:21:09 +00:00
  • b39e71ca2b Trying to fix cv_pls flatberg 2007-07-30 09:46:43 +00:00
  • 9ccdf97d07 Changed filenames of information content datasets. einarr 2007-07-30 07:55:36 +00:00
  • 1e18ac81de Added names to datasets. einarr 2007-07-30 07:54:22 +00:00
  • 349cab3c51 ups flatberg 2007-07-28 16:05:11 +00:00
  • 9a2e259209 c flatberg 2007-07-28 09:19:42 +00:00
  • df88f44255 clean up ups flatberg 2007-07-28 09:18:48 +00:00
  • 5cf34fc03f Added information content datasets. They are in files named ICs<subgraph><number> where those numbered 0 uses all ECs while 5 uses only the safest ones. einarr 2007-07-27 17:22:10 +00:00
  • 4b8f594966 app -> main.application flatberg 2007-07-27 09:40:58 +00:00
  • 47b89cc411 Fixed bug in esvd for m>n flatberg 2007-07-26 18:32:48 +00:00
  • 7fd4ac6225 pls opt fix flatberg 2007-07-26 18:32:27 +00:00
  • b35f814ef0 Added center check button on lineview flatberg 2007-07-26 18:26:50 +00:00
  • dc7f7dbde2 Added existing_identifiers function to Dataset. Added colouring drag'n'drop to DAGPlot in gobrowser module. einarr 2007-07-26 15:45:42 +00:00
  • a45743c31e Added main.py that now contains the One & Only Singleton instance of these classes: - 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. einarr 2007-07-26 12:35:59 +00:00
  • 91abf12f51 sd flatberg 2007-07-24 14:34:47 +00:00
  • 13dc6de5c1 Name annotations to go-terms. einarr 2007-07-24 13:34:40 +00:00
  • 1d517d0754 Changed hardcoded absolute path to relative path. einarr 2007-07-24 13:00:29 +00:00
  • 524c90fcf7 Updated to handle new numpy/scipy. einarr 2007-07-24 12:19:13 +00:00
  • 05274b4f0b confidence flatberg 2007-07-23 18:07:10 +00:00
  • 939dba20ee first import lpls flatberg 2007-07-23 17:35:28 +00:00
  • 54d271b841 go test data flatberg 2007-07-23 17:35:04 +00:00
  • a05d0faa0d Lib updates flatberg 2007-07-23 17:33:21 +00:00