source: orange-bioinformatics @ 1658:b31713e4c062

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Diff Rev Age Author Log Message
(edit) @1658:b31713e4c062   2 years markotoplak Merge.
(edit) @1657:edc96b23f6ef   2 years markotoplak Fixed a typo in code of PIPAx.
(edit) @1656:a6c7509a246b   2 years ales.erjavec Fixed OWGUI import in PIPAx widget
(edit) @1655:9d3ae06d69be   2 years mitar Added tag 2.5a1 for changeset 61fbdcb67aab
(edit) @1654:61fbdcb67aab   2 years mitar Merge.
(edit) @1653:508c7aa2e03c   2 years mitar Dependencies.
(edit) @1652:9d28a8edf5b9   2 years mitar Added distribute to dependencies.
(edit) @1651:37c90fb3cf5f   2 years mitar Changing description.
(edit) @1650:8008870c0a2d   2 years mitar Fixing manifest file.
(edit) @1649:2b0e1be1aeb5   2 years mitar This add-on is OS independent.
(edit) @1648:66f29a859110   2 years mitar Added dependency mirrors.
(edit) @1647:b6fe22253c86   2 years mitar Updated README.
(edit) @1646:8b2acc577189   2 years mitar Merge.
(edit) @1645:b542c4ab17b1   2 years mstajdohar Added help on install for developers.
(edit) @1644:e455af7d00bd   2 years mitar Fixing license text.
(edit) @1643:2cfa80dac3d3   2 years mitar Fixing some imports. Marking widgets as prototypes.
(edit) @1642:61aa6da18f78   2 years mitar Updating setup.py.
(edit) @1641:c1aeb79b5b4a   2 years mitar Automatically install setuptools if not present.
(edit) @1640:8fc4b69f2dcc   2 years mitar Removed Genome Map widget.
(edit) @1639:e3ff32a7c8da   2 years mitar Updated setup.py.
(edit) @1638:a9aacccb6d8a   2 years mitar Updating add-on description.
(edit) @1637:dde4ef52193b   2 years mitar Removing __file__ usage.
(edit) @1636:10d234fdadb9   2 years mitar Restructuring because we will not be using namespaces.
(edit) @1635:88033dab8187   2 years mitar Updated setup.py file.
(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 setup.py 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 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.
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