source: orange-bioinformatics @ 1583:2b90e7c95085

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Diff Rev Age Author Log Message
(edit) @1583:2b90e7c95085   2 years markotoplak Fixed a bug in obiGene (umatch did not work in Match objects). Gene set …
(edit) @1582:32734bec7ddd   2 years ales_erjavec Show a warning with a download link if suds is not installed.
(edit) @1581:877a0e7feba9   2 years ales_erjavec Fixed scene alignment (align left to prevent scene jittering when …
(edit) @1580:c4da7dfaf4db   2 years ales_erjavec Use Orange buffer dir for obiKEGG2 files.
(edit) @1579:364880120934   2 years ales_erjavec Only download the .xml kgml files in a separate thread, don't parse it …
(edit) @1578:9bc83a60db78   2 years markotoplak Gene matcher now have a call function and return a Match object, which …
(edit) @1577:5922a29becb8   2 years ales_erjavec Fixed some warnings.
(edit) @1576:10d0d6b92949   2 years ales_erjavec Fixed an error when initializing a GeneSet from an iterator.
(edit) @1575:3ddb8a20016d   2 years ales_erjavec Added obiKEGG2 package to the setup.py script.
(edit) @1574:fc0bf0206c8b   2 years ales_erjavec Added import of orngEnviron. Check the geneset taxids for valid ids.
(edit) @1573:f7cad4491971   2 years markotoplak Deduplicated code from obiExperiments in OWGenotypeDistances. …
(edit) @1572:b36656308a2c   2 years markotoplak Started obiGeneSetSig (new interface for gene set signatures) with Minca's …
(edit) @1571:0234560951c2   2 years markotoplak SetSig2 (which returns a domain) returns the same results as SetSig.
(edit) @1570:950a2fb24181   2 years markotoplak Prepared obiAssess for testing.
(edit) @1569:7898b2d279b2   2 years markotoplak obiGeneSets can now load gene sets from a dictionary or a list of pairs …
(edit) @1568:6f35074fbb48   2 years ales_erjavec Updated setup.py script
(edit) @1567:50498c102ac7   2 years ales_erjavec Fixed contextmanager generators. Disable widget GUI update on new data and …
(edit) @1566:6f61e6bfa9fc   2 years ales_erjavec Added some basic error warning reporting. Minor bug fixes.
(edit) @1565:ec5b8979e490   2 years markotoplak obiDicty: support for raw coverage.
(edit) @1564:0bb59b6fdc05   2 years ales_erjavec Fixed an error when receiving new (different) dataset due to non cleared …
(edit) @1563:003be1d1a365   2 years ales_erjavec Fixed a error with the use of filter function (needs to filter only Nones …
(edit) @1562:84cb6987b379   2 years ales_erjavec Code cleanup.
(edit) @1561:4769cbf80eca   2 years ales_erjavec Added caching of computed distances. Can now change the base for each …
(edit) @1560:94620f900411   2 years ales_erjavec Some code cleanup, added docstrings.
(edit) @1559:b40dd5c43beb   2 years ales_erjavec Moved Quality Control widget out of prototypes.
(edit) @1558:54642c2b4144   2 years ales_erjavec More work on Quality Control widget (now in semi-useful state).
(edit) @1557:cf24e5d3181b   2 years ales_erjavec Added obiExperiments module (functions from Genotype Distances widget).
(edit) @1556:b05260efcdf5   2 years ales_erjavec Added Quality Control widget prototype.
(edit) @1555:9422c051c5cf   2 years markotoplak Orange.data.variable -> Orange.feature
(edit) @1554:c965b96e5c41   2 years ales_erjavec Pre cache pathways, using (KEGG, pathways) gene set hierarchy.
(edit) @1553:c0221fcbf175   2 years ales_erjavec Added comment to requests use of keep-alive.
(edit) @1552:736722ec7ff6   2 years ales_erjavec Fixed taxid mapping in to_taxid function.
(edit) @1551:a5c02ae75573   2 years ales_erjavec Include class name in the warning.
(edit) @1550:9226929348de   2 years ales_erjavec Removed unneeded imports, fixed some errors.
(edit) @1549:bff566fa42dc   2 years ales_erjavec obiGeneSets.keggGeneSets now uses obiKEGG2.
(edit) @1548:80b9e523116b   2 years ales_erjavec Fixed and added some tests for obiKEGG2
(edit) @1547:1420f13cba63   2 years ales_erjavec Changed default configuration.
(edit) @1546:ddd6bfae87e9   2 years ales_erjavec Added EnzymeEntry class.
(edit) @1545:3fedad365f74   2 years ales_erjavec Fixed name matcher aliases version.
(edit) @1544:1bfc93a9bc5d   2 years ales_erjavec Fixed binfo api method (return None not 'None')
(edit) @1543:6481dba93e2e   2 years ales_erjavec get_entries_by_type returns a list, renamed cache filename.
(edit) @1542:850adb56ad5a   2 years ales_erjavec Fixed open method (must return a fp like object).
(edit) @1541:efd40e75bc7d   2 years ales_erjavec Added optional suds.transport.Transport subclass using requests package.
(edit) @1540:90209537a0e1   2 years ales_erjavec Small speedup of get_enriched_pathways.
(edit) @1539:4d0cb852d2cd   2 years ales_erjavec If the batch has invalid ids try bisection of the ids.
(edit) @1538:1241665d4e60   2 years ales_erjavec Fixing errors in get and batch_get.
(edit) @1537:3a5221cffda5   2 years ales_erjavec Replacing the old value in setitem method.
(edit) @1536:8212c4a2204e   2 years ales_erjavec Using batch_get method in iteritems, itervalues methods.
(edit) @1535:50a0227812f7   2 years ales_erjavec Added batch_get method to DBDataBase class.
(edit) @1534:013203e8fa81   2 years ales_erjavec KEGG widget now using the new web services interface
(edit) @1533:8543e989a290   2 years ales_erjavec Added tests dir with unittests for obiKEGG2
(edit) @1532:14a377419a09   2 years ales_erjavec Added KEGG interface using web services
(edit) @1531:54a9507c7ee4   2 years ales_erjavec Added traversal methods, term_by_name.
(edit) @1530:48dc3a3e2cac   2 years ales_erjavec Fixed docstrings, typos.
(edit) @1529:702241c4efb9   2 years www-data Automated manifest update.
(edit) @1528:911c336b6c08   2 years ales.erjavec Fixed docstrings (orngNetwork.Network -> Orange.network.Graph)
(edit) @1527:66a207e0663b   2 years ales.erjavec Now using Orange.network.Graph.
(edit) @1526:13f22da4c040   2 years www-data Automated manifest update.
(edit) @1525:669aad39c027   2 years ales.erjavec Added save graph button.
(edit) @1524:c2887cc2bd9f   2 years www-data Automated manifest update.
(edit) @1523:8d72a620e865   2 years ales.erjavec Moved obiPPI import down the module due to a cyclic import dependency.
(edit) @1522:2c0b80893991   2 years www-data Automated manifest update.
(edit) @1521:19233258515f   2 years markotoplak OWPIPA: added Experiment field.
(edit) @1520:d522cab1fe25   2 years www-data Automated manifest update.
(edit) @1519:b5ea81f44308   2 years ales.erjavec Fixed the ncbi omim download path.
(edit) @1518:7d6bb59c6ac3   2 years www-data Automated manifest update.
(edit) @1517:eeebac5bf699   2 years ales.erjavec Split the source string.
(edit) @1516:2f10cfec106b   2 years www-data Automated manifest update.
(edit) @1515:3e79683f4ab6   2 years ales.erjavec Added PPI domain.
(edit) @1514:912706a3f472   2 years ales.erjavec Renamed STRINGNonCommercial to STRINGDetailed.
(edit) @1513:b8e8fbe0b29f   2 years www-data Automated manifest update.
(edit) @1512:c4a1ed0a9f8a   2 years ales.erjavec Added STRINGNonCommercial class.
(edit) @1511:9d3bb3ff4458   2 years www-data Automated manifest update.
(edit) @1510:058ce9a71723   2 years markotoplak obiDicty: support for coverage.
(edit) @1509:7e8fadd4ef33   2 years www-data Automated manifest update.
(edit) @1508:47a3ae04bc5d   2 years ales.erjavec Added search_id method implementations for BioGRID and STRING.
(edit) @1507:db0058df9281   2 years www-data Automated manifest update.
(edit) @1506:beecaafe2d7f   2 years markotoplak obiProb: FDR now allows unsorted lists on input. Regain old performance …
(edit) @1505:5219ca026490   2 years www-data Automated manifest update.
(edit) @1504:ce65c16ede61   2 years ales.erjavec Added PPIDatabase like interface for GeneMania.
(edit) @1503:8a0169e408e1   2 years www-data Automated manifest update.
(edit) @1502:96417e153a3d   2 years ales.erjavec Added all_edges_annotated interface to PPIDatabase.
(edit) @1501:d6ac9c96e4b0   2 years www-data Automated manifest update.
(edit) @1500:d7d4664afe01   2 years ales.erjavec Added progress_callback parameter to gene_expression_atlas and …
(edit) @1499:ccc33c0cb5de   3 years www-data Automated manifest update.
(edit) @1498:20bf9f96189e   3 years ales.erjavec Fixed a broken filters GUI. Fixed a problem with PyQt4 and sorting in …
(edit) @1497:08fad7893ad2   3 years www-data Automated manifest update.
(edit) @1496:f34d9864f0f6   3 years ales.erjavec Fixed download function for STRING.
(edit) @1495:3ab2f3d8a4e5   3 years ales.erjavec Added update script for STRING database. Some minor fixes to …
(edit) @1494:f7f4449de0fb   3 years www-data Automated manifest update.
(edit) @1493:097b6aec83e9   3 years ales.erjavec Fixed download function for STRING.
(edit) @1492:39b580f94718   3 years www-data Automated manifest update.
(edit) @1491:465aaa713232   3 years ales.erjavec Fixed some errors while initializing the db for STRING. Implemented the …
(edit) @1490:1d7dc05b79e1   3 years www-data Automated manifest update.
(edit) @1489:9b78d97eb300   3 years markotoplak OWGenotypeDistances: chips are in red when they are possibly ambiguous
(edit) @1488:402d442f10ee   3 years www-data Automated manifest update.
(edit) @1487:a19de361ce52   3 years ales.erjavec Changed STRING base url (the old one with port 8080 stopped responding).
(edit) @1486:0ba78bbd22dc   3 years www-data Automated manifest update.
(edit) @1485:6b33e3056722   3 years markotoplak OWGenotypeDistances: .
(edit) @1484:eb5d88b94c45   3 years markotoplak OWGenotypeDistances: user interface now shows clearly what the output is …
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