source: orange-bioinformatics @ 1773:5e6e42c393a9

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Diff Rev Age Author Log Message
(edit) @1773:5e6e42c393a9   11 months markotoplak Small changes to miRNA update scripts. Added title and tags to elements …
(edit) @1772:58718fc3f736   11 months markotoplak obiGeneSetSig: CORG were build a gene too large (fixed). SetSig has the …
(edit) @1771:bf833fa5d2a3   12 months ales.erjavec Fixed 'Ontology' and 'Annotations' stream parsing.
(edit) @1770:48af55b8e628   12 months ales.erjavec 'Ontology.getitem' now raises a KeyError for an unknown term id.
(edit) @1769:c0c6b64879cf   12 months ales.erjavec Filter out terms from the annotations that are not present in the …
(edit) @1768:9cb38945684f   12 months ales.erjavec Removed deprecated and nonfunctioning 'drawEnrichmentGraph_tostream' …
(edit) @1767:214b1db4e31a   12 months ales.erjavec obiGO code style fixes.
(edit) @1766:7508cfe5ad26   12 months vid.flashpoint Added
(edit) @1765:b497b961c944   12 months vid.flashpoint Added
(edit) @1764:04eaaffe6804   12 months vid.flashpoint Merged biolab/orange-bioinformatics into default
(edit) @1763:896de921cd4b   12 months vid.flashpoint Fixed several syntax errors
(edit) @1762:12c8aae24310   12 months vid.flashpoint Deleted unused imports
(edit) @1761:d8f3d4bb64fa   12 months vid.flashpoint Added
(edit) @1760:165df4199ec9   12 months ales.erjavec Optimized DBDatabase batch_get/pre_cache w.r.t. number of separate network …
(edit) @1759:28ae945028d1   12 months markotoplak Deleted an obsolete update script.
(edit) @1758:338084e4c84e   12 months markotoplak Removed KEGG as the current KEGG script does not uses serverfiles.
(edit) @1757:1aee9d34655b   12 months ales.erjavec Disabled automatic cache invalidation.
(edit) @1756:ec01f8aa98a9   12 months markotoplak STRING database build: do not unzip files.
(edit) @1755:418d0e7f330a   12 months markotoplak Merge.
(edit) @1754:56ba93b2b1e1   12 months markotoplak Update scripts: warn if username and password are not passed.
(edit) @1753:d8bea5b19e25   12 months markotoplak Update script for STRING: reads current version from the webpage and …
(edit) @1752:9932018b0728   12 months markotoplak Update script for gene sets.
(edit) @1751:a3db39d180ab   12 months ales.erjavec Fixed KEGG Pathway Browser organism list initialization.
(edit) @1750:8a7cd2cf4ea2   12 months ales.erjavec Using a single global Genome instance in obiKEGG module level functions.
(edit) @1749:29a979e9bf4d   12 months ales.erjavec Optimized Gsea widget organism list initialization.
(edit) @1748:3a6c3d41aaee   12 months ales.erjavec Test for the presence of 'self.signalManager'. A default global …
(edit) @1747:fee3c71716ef   12 months markotoplak KEGG organism name finding fixes.
(edit) @1746:54b84bf6d1a4   12 months ales.erjavec Deleted old and obsolete module
(edit) @1745:8b2d53ec3523   12 months ales.erjavec Fixed 'organism_name_search' method.
(edit) @1744:fad34df9e962   12 months ales.erjavec Moved old obiKEGG tests inside the obiKEGG package.
(edit) @1743:9f18a1e0657c   12 months ales.erjavec Extended term name mangling to all python reserved keywords.
(edit) @1742:fa3a9e4af7e6   12 months ales.erjavec Code style and docstring fixes.
(edit) @1741:1c2feb7cd8d2   12 months ales.erjavec Added 'prefix' parameter for KEGG Pathway database interface.
(edit) @1740:0ef1058694a2   12 months ales.erjavec Try guessing the gene attribute name.
(edit) @1739:939281048915   12 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   17 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   19 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 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   20 months markotoplak Speed up PCA and PLS (obiGeneSetSig).
(edit) @1708:c442e936f1ef   20 months markotoplak Another speedup of SetSig. Now it is 30% faster on with …
(edit) @1707:7d692228fea1   20 months markotoplak Speed up of setsig (obiGeneSetSig).
(edit) @1706:fee5567c52af   20 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   21 months ales.erjavec Fixed wrong relative import.
(edit) @1703:3b1a95ba16ec   21 months markotoplak gene matching: using generators for set_targets input now works correctly
(edit) @1702:2010380147ce   22 months ales.erjavec Added svg icons to
(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   22 months mitar Added tag 2.5a5 for changeset f8e82ecc8ae5
(edit) @1684:f8e82ecc8ae5   22 months mitar Version bump.
(edit) @1683:3c74a8c23b4b   22 months mitar Shortening namespace.
(edit) @1682:2e2c671e4300   22 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.
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