source: orange-bioinformatics @ 1634:32373d957326

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Diff Rev Age Author Log Message
(edit) @1634:32373d957326   2 years mitar Renamed addon reference documentation.
(edit) @1633:b8852fdd1a0f   2 years mitar Fixing imports.
(edit) @1632:9cf919d0f343   2 years mitar Fixing imports.
(edit) @1631:45bbfc8ab14c   2 years mitar Moving scripts.
(edit) @1630:bac3c4d73e0d   2 years mitar Updated readme file.
(edit) @1629:0d6de7936e04   2 years mitar Moving files around.
(edit) @1628:51f6cf677c61   2 years mitar Adding license text.
(edit) @1627:c195b0069f53   2 years mitar Not needed anymore. We will be using eggs.
(edit) @1626:10d512c242a9   2 years mitar We already have a license text.
(edit) @1625:cefeb35cbfc9   2 years mitar Moving files around.
(edit) @1624:145bc5b1550e   2 years mitar Cleaning tags.
(edit) @1623:186d828e3699   2 years mitar Renamed documentation directory.
(edit) @1622:3d2f34a594e5   2 years ales.erjavec Handle an invalid selected index from the label combo box.
(edit) @1621:dad955df95e8   2 years ales.erjavec Open dictyExpress links with selected genes only.
(edit) @1620:5901c58464eb   2 years ales.erjavec Sort ids before querying PIPAx api (oherwise the columns can get …
(edit) @1619:3ddf83d9d93b   2 years ales.erjavec Fixed a major error handing the downloaded gene list (all reported gene …
(edit) @1618:56ed7843a919   2 years ales.erjavec Fixed date formating (using locale's date representation).
(edit) @1617:a67c39dc9477   2 years ales.erjavec Copied SelectionByKey class from OWPIPA into OWPIPAx (problems with …
(edit) @1616:6c0bc463ca9b   2 years ales.erjavec Added new PIPAx widget.
(edit) @1615:8506076ec2e7   2 years ales.erjavec Added PIPAx api interface.
(edit) @1614:b8ee06613d54   2 years ales.erjavec Added columns from the gene info view to the output.
(edit) @1613:c3560c335bf9   2 years ales.erjavec Changed results from the GeneAtlas REST api. Added cache versioning.
(edit) @1612:6935f946a4f6   2 years ales.erjavec Orange.projection.pca.Pca -> Orange.projection.linear.PCA
(edit) @1611:3b33933bd2c7   2 years ales.erjavec Fixed progress_bar_milestones import.
(edit) @1610:f6c73952d74f   2 years ales.erjavec Save download file to a temporary '.part' file.
(edit) @1609:6b0bb985598f   2 years ales.erjavec Can now specify specific annotation and ontology revision.
(edit) @1608:bb559485a499   2 years lan.zagar Handle different line endings (see #1160).
(edit) @1607:1daf61f47beb   2 years markotoplak Added ASSESS to obiGeneSetSig.
(edit) @1606:610975979e42   2 years ales.erjavec Added 'Clear cache' button, small fixes to progress reporting.
(edit) @1605:efd5ac5a1579   2 years ales.erjavec Added clear_cache function.
(edit) @1604:e53326641eb0   2 years ales.erjavec Cache invalidation of kgml files.
(edit) @1603:7a78a7302c20   2 years ales.erjavec Configurable cache invalidation.
(edit) @1602:d55a75faef7a   2 years ales.erjavec Fixed obiKEGG conf.
(edit) @1601:d3a65a71731e   2 years markotoplak Fixes supporting the move of (most of) Orange.misc to Orange.utils.
(edit) @1600:60f301f74126   2 years markotoplak Added CORGs to obiGeneSetSig.
(edit) @1599:d26971fdd077   2 years markotoplak obiGeneSetSig: refactoring.
(edit) @1598:fda2dc9e724e   2 years markotoplak Some refactoring of obiGeneSetSig.
(edit) @1597:574fe4f8d1d3   2 years markotoplak Added GSA to obiGeneSetSig.
(edit) @1596:ac353555dee3   2 years ales.erjavec Removed str.format for Python 2.5.
(edit) @1595:8ef1b76b2e6d   2 years markotoplak Added PLS to obiGeneSetSig.
(edit) @1594:98ff35c02b40   2 years markotoplak Refactoring of obiGeneSetSig.
(edit) @1593:f888bd8a5ae2   2 years markotoplak Added PCA transformation to obiGeneSetSig.
(edit) @1592:c39f563cc473   2 years markotoplak Added Mean and Median to the new gene set signatures module.
(edit) @1591:cd329b25dfc3   2 years ales.erjavec Deleted old GOLib licenese.
(edit) @1590:8752cd1309cd   2 years ales.erjavec Cosmetic changes.
(edit) @1589:d223e294380d   2 years ales.erjavec Added LICENSE.txt
(edit) @1588:7141bf292e06   2 years ales.erjavec A workaround for a bug in setuptools.
(edit) @1587:c29c74349ecc   2 years markotoplak Added caching of gene matchers.
(edit) @1586:1d9e9b337b71   2 years ales.erjavec Added tag 1.1a for changeset 973f84dca0f2
(edit) @1585:973f84dca0f2   2 years ales.erjavec Cleanup script, use setuptools if available.
(edit) @1584:56076decfd54   2 years markotoplak Trivial merge.
(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 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 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.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.
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