source: orange-bioinformatics @ 1595:8ef1b76b2e6d

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Diff Rev Age Author Log Message
(edit) @1595:8ef1b76b2e6d   15 months markotoplak Added PLS to obiGeneSetSig.
(edit) @1594:98ff35c02b40   15 months markotoplak Refactoring of obiGeneSetSig.
(edit) @1593:f888bd8a5ae2   15 months markotoplak Added PCA transformation to obiGeneSetSig.
(edit) @1592:c39f563cc473   15 months markotoplak Added Mean and Median to the new gene set signatures module.
(edit) @1591:cd329b25dfc3   15 months ales.erjavec Deleted old GOLib licenese.
(edit) @1590:8752cd1309cd   15 months ales.erjavec Cosmetic changes.
(edit) @1589:d223e294380d   15 months ales.erjavec Added LICENSE.txt
(edit) @1588:7141bf292e06   15 months ales.erjavec A workaround for a bug in setuptools.
(edit) @1587:c29c74349ecc   15 months markotoplak Added caching of gene matchers.
(edit) @1586:1d9e9b337b71   15 months ales.erjavec Added tag 1.1a for changeset 973f84dca0f2
(edit) @1585:973f84dca0f2   15 months ales.erjavec Cleanup setup.py script, use setuptools if available.
(edit) @1584:56076decfd54   15 months markotoplak Trivial merge.
(edit) @1583:2b90e7c95085   15 months markotoplak Fixed a bug in obiGene (umatch did not work in Match objects). Gene set …
(edit) @1582:32734bec7ddd   15 months ales_erjavec Show a warning with a download link if suds is not installed.
(edit) @1581:877a0e7feba9   15 months ales_erjavec Fixed scene alignment (align left to prevent scene jittering when …
(edit) @1580:c4da7dfaf4db   15 months ales_erjavec Use Orange buffer dir for obiKEGG2 files.
(edit) @1579:364880120934   15 months ales_erjavec Only download the .xml kgml files in a separate thread, don't parse it …
(edit) @1578:9bc83a60db78   15 months markotoplak Gene matcher now have a call function and return a Match object, which …
(edit) @1577:5922a29becb8   15 months ales_erjavec Fixed some warnings.
(edit) @1576:10d0d6b92949   15 months ales_erjavec Fixed an error when initializing a GeneSet from an iterator.
(edit) @1575:3ddb8a20016d   15 months ales_erjavec Added obiKEGG2 package to the setup.py script.
(edit) @1574:fc0bf0206c8b   15 months ales_erjavec Added import of orngEnviron. Check the geneset taxids for valid ids.
(edit) @1573:f7cad4491971   15 months markotoplak Deduplicated code from obiExperiments in OWGenotypeDistances. …
(edit) @1572:b36656308a2c   15 months markotoplak Started obiGeneSetSig (new interface for gene set signatures) with Minca's …
(edit) @1571:0234560951c2   15 months markotoplak SetSig2 (which returns a domain) returns the same results as SetSig.
(edit) @1570:950a2fb24181   15 months markotoplak Prepared obiAssess for testing.
(edit) @1569:7898b2d279b2   15 months markotoplak obiGeneSets can now load gene sets from a dictionary or a list of pairs …
(edit) @1568:6f35074fbb48   16 months ales_erjavec Updated setup.py script
(edit) @1567:50498c102ac7   16 months ales_erjavec Fixed contextmanager generators. Disable widget GUI update on new data and …
(edit) @1566:6f61e6bfa9fc   16 months ales_erjavec Added some basic error warning reporting. Minor bug fixes.
(edit) @1565:ec5b8979e490   16 months markotoplak obiDicty: support for raw coverage.
(edit) @1564:0bb59b6fdc05   16 months ales_erjavec Fixed an error when receiving new (different) dataset due to non cleared …
(edit) @1563:003be1d1a365   16 months ales_erjavec Fixed a error with the use of filter function (needs to filter only Nones …
(edit) @1562:84cb6987b379   16 months ales_erjavec Code cleanup.
(edit) @1561:4769cbf80eca   16 months ales_erjavec Added caching of computed distances. Can now change the base for each …
(edit) @1560:94620f900411   16 months ales_erjavec Some code cleanup, added docstrings.
(edit) @1559:b40dd5c43beb   16 months ales_erjavec Moved Quality Control widget out of prototypes.
(edit) @1558:54642c2b4144   16 months ales_erjavec More work on Quality Control widget (now in semi-useful state).
(edit) @1557:cf24e5d3181b   16 months ales_erjavec Added obiExperiments module (functions from Genotype Distances widget).
(edit) @1556:b05260efcdf5   16 months ales_erjavec Added Quality Control widget prototype.
(edit) @1555:9422c051c5cf   16 months markotoplak Orange.data.variable -> Orange.feature
(edit) @1554:c965b96e5c41   16 months ales_erjavec Pre cache pathways, using (KEGG, pathways) gene set hierarchy.
(edit) @1553:c0221fcbf175   16 months ales_erjavec Added comment to requests use of keep-alive.
(edit) @1552:736722ec7ff6   16 months ales_erjavec Fixed taxid mapping in to_taxid function.
(edit) @1551:a5c02ae75573   16 months ales_erjavec Include class name in the warning.
(edit) @1550:9226929348de   16 months ales_erjavec Removed unneeded imports, fixed some errors.
(edit) @1549:bff566fa42dc   16 months ales_erjavec obiGeneSets.keggGeneSets now uses obiKEGG2.
(edit) @1548:80b9e523116b   16 months ales_erjavec Fixed and added some tests for obiKEGG2
(edit) @1547:1420f13cba63   16 months ales_erjavec Changed default configuration.
(edit) @1546:ddd6bfae87e9   16 months ales_erjavec Added EnzymeEntry class.
(edit) @1545:3fedad365f74   16 months ales_erjavec Fixed name matcher aliases version.
(edit) @1544:1bfc93a9bc5d   16 months ales_erjavec Fixed binfo api method (return None not 'None')
(edit) @1543:6481dba93e2e   16 months ales_erjavec get_entries_by_type returns a list, renamed cache filename.
(edit) @1542:850adb56ad5a   16 months ales_erjavec Fixed open method (must return a fp like object).
(edit) @1541:efd40e75bc7d   16 months ales_erjavec Added optional suds.transport.Transport subclass using requests package.
(edit) @1540:90209537a0e1   16 months ales_erjavec Small speedup of get_enriched_pathways.
(edit) @1539:4d0cb852d2cd   16 months ales_erjavec If the batch has invalid ids try bisection of the ids.
(edit) @1538:1241665d4e60   16 months ales_erjavec Fixing errors in get and batch_get.
(edit) @1537:3a5221cffda5   16 months ales_erjavec Replacing the old value in setitem method.
(edit) @1536:8212c4a2204e   16 months ales_erjavec Using batch_get method in iteritems, itervalues methods.
(edit) @1535:50a0227812f7   16 months ales_erjavec Added batch_get method to DBDataBase class.
(edit) @1534:013203e8fa81   16 months ales_erjavec KEGG widget now using the new web services interface
(edit) @1533:8543e989a290   16 months ales_erjavec Added tests dir with unittests for obiKEGG2
(edit) @1532:14a377419a09   16 months ales_erjavec Added KEGG interface using web services
(edit) @1531:54a9507c7ee4   16 months ales_erjavec Added traversal methods, term_by_name.
(edit) @1530:48dc3a3e2cac   16 months ales_erjavec Fixed docstrings, typos.
(edit) @1529:702241c4efb9   16 months www-data Automated manifest update.
(edit) @1528:911c336b6c08   16 months ales.erjavec Fixed docstrings (orngNetwork.Network -> Orange.network.Graph)
(edit) @1527:66a207e0663b   16 months ales.erjavec Now using Orange.network.Graph.
(edit) @1526:13f22da4c040   18 months www-data Automated manifest update.
(edit) @1525:669aad39c027   18 months ales.erjavec Added save graph button.
(edit) @1524:c2887cc2bd9f   18 months www-data Automated manifest update.
(edit) @1523:8d72a620e865   18 months ales.erjavec Moved obiPPI import down the module due to a cyclic import dependency.
(edit) @1522:2c0b80893991   18 months www-data Automated manifest update.
(edit) @1521:19233258515f   18 months markotoplak OWPIPA: added Experiment field.
(edit) @1520:d522cab1fe25   18 months www-data Automated manifest update.
(edit) @1519:b5ea81f44308   18 months ales.erjavec Fixed the ncbi omim download path.
(edit) @1518:7d6bb59c6ac3   18 months www-data Automated manifest update.
(edit) @1517:eeebac5bf699   18 months ales.erjavec Split the source string.
(edit) @1516:2f10cfec106b   18 months www-data Automated manifest update.
(edit) @1515:3e79683f4ab6   18 months ales.erjavec Added PPI domain.
(edit) @1514:912706a3f472   18 months ales.erjavec Renamed STRINGNonCommercial to STRINGDetailed.
(edit) @1513:b8e8fbe0b29f   18 months www-data Automated manifest update.
(edit) @1512:c4a1ed0a9f8a   18 months ales.erjavec Added STRINGNonCommercial class.
(edit) @1511:9d3bb3ff4458   19 months www-data Automated manifest update.
(edit) @1510:058ce9a71723   19 months markotoplak obiDicty: support for coverage.
(edit) @1509:7e8fadd4ef33   19 months www-data Automated manifest update.
(edit) @1508:47a3ae04bc5d   19 months ales.erjavec Added search_id method implementations for BioGRID and STRING.
(edit) @1507:db0058df9281   19 months www-data Automated manifest update.
(edit) @1506:beecaafe2d7f   19 months markotoplak obiProb: FDR now allows unsorted lists on input. Regain old performance …
(edit) @1505:5219ca026490   19 months www-data Automated manifest update.
(edit) @1504:ce65c16ede61   19 months ales.erjavec Added PPIDatabase like interface for GeneMania.
(edit) @1503:8a0169e408e1   19 months www-data Automated manifest update.
(edit) @1502:96417e153a3d   19 months ales.erjavec Added all_edges_annotated interface to PPIDatabase.
(edit) @1501:d6ac9c96e4b0   19 months www-data Automated manifest update.
(edit) @1500:d7d4664afe01   19 months ales.erjavec Added progress_callback parameter to gene_expression_atlas and …
(edit) @1499:ccc33c0cb5de   20 months www-data Automated manifest update.
(edit) @1498:20bf9f96189e   20 months ales.erjavec Fixed a broken filters GUI. Fixed a problem with PyQt4 and sorting in …
(edit) @1497:08fad7893ad2   20 months www-data Automated manifest update.
(edit) @1496:f34d9864f0f6   20 months ales.erjavec Fixed download function for STRING.
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