source: orange-bioinformatics @ 1743:9f18a1e0657c

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Diff Rev Age Author Log Message
(edit) @1743:9f18a1e0657c   13 months ales.erjavec Extended term name mangling to all python reserved keywords.
(edit) @1742:fa3a9e4af7e6   13 months ales.erjavec Code style and docstring fixes.
(edit) @1741:1c2feb7cd8d2   13 months ales.erjavec Added 'prefix' parameter for KEGG Pathway database interface.
(edit) @1740:0ef1058694a2   13 months ales.erjavec Try guessing the gene attribute name.
(edit) @1739:939281048915   13 months ales.erjavec KEGG Pathways widget code style fixes
(edit) @1738:1f7725e12b25   13 months ales.erjavec Fixed 'organism_name_search' for KEGG Genome ids.
(edit) @1737:729925f75820   13 months ales.erjavec KEGG bug fixes.
(edit) @1736:b3b664abcfdd   13 months ales.erjavec Added sphinx rst documentation for obiKEGG.
(edit) @1735:50499d1dc55a   13 months ales.erjavec Changed the Organism.gene_aliases method.
(edit) @1734:91d14dd2cf0e   14 months ales.erjavec obiKEGG code style fixes.
(edit) @1733:548d1187a29f   14 months ales.erjavec Porting obiKEGG to use the new REST KEGG API.
(edit) @1732:aa2f36ae4cc7   14 months ales.erjavec Merge
(edit) @1731:23ece30de348   14 months ales.erjavec Changed 'orange.Orange' to 'orange.OrangeBase'.
(edit) @1730:5a94804de6eb   14 months ales.erjavec Added category description for the new canvas interface.
(edit) @1729:cfd3723ae0c6   15 months ales.erjavec Added svg icon for Databases widget.
(edit) @1728:a7d42a8d1ed2   14 months markotoplak Added an option in Assess to not ignore umatchable context.
(edit) @1727:9cb1de35eb56   17 months ales.erjavec Create the destination directory if it does not exist.
(edit) @1726:6778e0225b86   17 months ales.erjavec Added new icons by Peter Cuhalev and replaced existing ones with expanded …
(edit) @1725:1c834422f29e   17 months markotoplak obiGeneSetSig: assess now works even if gene matcher did not perfectly …
(edit) @1724:539bf92eeaab   18 months markotoplak Version bump.
(edit) @1723:753e1d554488   18 months markotoplak SetSig uses statc for pearsonr. Around 10x speedup compared to numpy.
(edit) @1722:70df6521f068   19 months markotoplak updatemiRNA script now also works.
(edit) @1721:921b3780c6cc   20 months markotoplak Moved common functionality of the server files update scripts to a …
(edit) @1720:354d91b1af9f   20 months markotoplak Fixed update scripts for STRING and Taxonomy.
(edit) @1719:6e8861564778   20 months markotoplak Fixed update scripts for MeSH, GO, HomoloGene, NCBI_geneinfo, OMIM, PPI. …
(edit) @1718:146dc04e42de   20 months markotoplak Removed KEGG update scripts, updated (and ran) dicty base and GEO.
(edit) @1717:b9f395780e75   20 months markotoplak Copied server update scripts from Orange source.
(edit) @1716:4c4266f7c5a5   20 months markotoplak Removed the old version of obiKEGG. Renamed obiKEGG2 -> obiKEGG.
(edit) @1715:87468c6e6443   20 months markotoplak Removed use of the old obiKEGG module. Hacked a REST version for gene …
(edit) @1714:cdad13f0d034   20 months markotoplak Updated the description.
(edit) @1713:7113883f4437   20 months markotoplak Fixes for obiGeneSets. Compatible files were generated and uploaded to SF.
(edit) @1712:bcd52ead3d93   20 months markotoplak Classes for storing gene set data moved to Orange.bio.geneset. obiGeneSets …
(edit) @1711:643d37885055   20 months markotoplak obiGeneSetSig: speedup of ASSESS.
(edit) @1710:b36fc0b5814c   20 months ales.erjavec Added 'Enrichment Report' output to the GO Browser widget.
(edit) @1709:d9f0ae5a3c67   21 months markotoplak Speed up PCA and PLS (obiGeneSetSig).
(edit) @1708:c442e936f1ef   21 months markotoplak Another speedup of SetSig. Now it is 30% faster on DLBCL.tab with …
(edit) @1707:7d692228fea1   21 months markotoplak Speed up of setsig (obiGeneSetSig).
(edit) @1706:fee5567c52af   21 months markotoplak Make the datasets with joined class values picklable.
(edit) @1705:0b6781662f02   21 months markotoplak obiGsea.takeClasses: now builds a class value with get_value_from.
(edit) @1704:8480e307a8a0   22 months ales.erjavec Fixed wrong relative import.
(edit) @1703:3b1a95ba16ec   22 months markotoplak gene matching: using generators for set_targets input now works correctly
(edit) @1702:2010380147ce   22 months ales.erjavec Added svg icons to MANIFEST.in
(edit) @1701:761bf570c1f4   22 months ales.erjavec Added SVG icons for some widgets.
(edit) @1700:b2d2ea27545d   22 months ales.erjavec Fixed relative import.
(edit) @1699:d7fa537b163e   22 months ales.erjavec Moved Gene Atlas Tissue Expression widget out of prototypes.
(edit) @1698:66f083dd6a1b   22 months lan.zagar Save settings in Atlas widget.
(edit) @1697:1c6e4093f56a   22 months ales.erjavec Activate selection in ScoreHist to enable interactive cutoff.
(edit) @1696:dea5ec1c3800   22 months ales.erjavec Added tag 2.5a6 for changeset ecd9bb9628ea
(edit) @1695:ecd9bb9628ea   22 months ales.erjavec Version bump.
(edit) @1694:a240c6650b8e   22 months ales.erjavec BUGFIX. Fixed cache version invalidation. Must close the shelve before …
(edit) @1693:d9eebf8944ec   22 months ales.erjavec BUGFIX. Removed a failing redundant import. Creating a new obiTaxonomy …
(edit) @1692:66a285f2e160   22 months lan.zagar Hopefully fixes #1208 for good.
(edit) @1691:d2aeb3889a90   22 months markotoplak CV feature build for obiGeneSetSig.
(edit) @1690:cba131a6a0c5   22 months markotoplak obiGeneSetSig: small changes in the interface.
(edit) @1689:f3edbd78dbfd   22 months ales.erjavec Check the target selection for a case where there are no labels/values. …
(edit) @1688:11472cddba90   22 months ales.erjavec Added Array Express widget.
(edit) @1687:460a66cfdc01   22 months ales.erjavec Basic annotations for data table features (Charecteristics, …
(edit) @1686:c47c9865d9bc   22 months markotoplak Bump the version of obiDicty buffer.
(edit) @1685:2be01ac7a2be   23 months mitar Added tag 2.5a5 for changeset f8e82ecc8ae5
(edit) @1684:f8e82ecc8ae5   23 months mitar Version bump.
(edit) @1683:3c74a8c23b4b   23 months mitar Shortening namespace.
(edit) @1682:2e2c671e4300   23 months lan.zagar Replaced split(\n) with splitlines (closes #1160).
(edit) @1681:d8249ba65b73   23 months markotoplak OWPIPA: changed default expression type (Gadi's recommendation).
(edit) @1680:47391b3c2532   23 months markotoplak Fixed last commit.
(edit) @1679:acc78615f489   23 months markotoplak PIPAx: downloading data now uses buffers (removed reload=reload from calls …
(edit) @1678:9fc829170a8f   23 months mitar Exec bit.
(edit) @1677:2db135e7ff3f   23 months mitar Also include documentation in source package.
(edit) @1676:b7daa12c2b33   2 years mitar This doesn't work.
(edit) @1675:1b8a5783fa86   2 years mitar Added tag 2.5a4 for changeset 1feec0bd5ffb
(edit) @1674:1feec0bd5ffb   2 years mitar Documentation changes. Version bump.
(edit) @1673:bfb162916b57   2 years mitar Added tag 2.5a3 for changeset 451a2de7c9d7
(edit) @1672:451a2de7c9d7   2 years mitar Version bump.
(edit) @1671:7ee0e13bc0a4   2 years mitar Fixed package classifiers and keywords.
(edit) @1670:a23a5f7825b0   2 years mitar Added tag 2.5a2 for changeset a6bc72ca3aae
(edit) @1669:a6bc72ca3aae   2 years mitar Version bump.
(edit) @1668:a9eb1a590d6b   2 years mitar More on documentation.
(edit) @1667:c4c652ff9d24   2 years mitar Missed in renaming.
(edit) @1666:15208881edf4   2 years mitar Renaming documentation.
(edit) @1665:9608dd9c7656   2 years mitar Unifying documentation.
(edit) @1664:ab62a9259105   2 years mitar Reference should have modindex.
(edit) @1663:6f48078a9554   2 years mitar Merge.
(edit) @1662:427f1876f3e6   2 years mitar Revamped documentation.
(edit) @1661:6c5f448f2563   2 years mitar Moved style CSS file.
(edit) @1660:d30ab3fdb2f2   2 years mitar Version bump.
(edit) @1659:32e069184b7d   2 years ales.erjavec Replaced 'distribute' dependency with setuptools'. Trimmed dependencies.
(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.
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