source: orange-bioinformatics @ 1798:f1e73901a1d3

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Diff Rev Age Author Log Message
(edit) @1798:f1e73901a1d3   11 months vid.flashpoint Added Reactome Pathways genesets for humans
(edit) @1797:43f9097a0bc8   11 months vid.flashpoint is now correctly updated
(edit) @1796:a8618bd60eb7   11 months vid.flashpoint Merged latest commit
(edit) @1795:663192bd4469   11 months vid.flashpoint Removed and created genesets in …
(edit) @1794:3a530b619d7f   11 months vid.flashpoint Added Cytobands genesets and modified Both need some extra …
(edit) @1793:5dfeaff02331   11 months vid.flashpoint P-values greater than 0.001 are now displayed with regular notation in the …
(edit) @1792:89d57e897273   11 months vid.flashpoint Added a documentation entry for
(edit) @1791:8e343fc769be   11 months vid.flashpoint Sorting according to p-values works.
(edit) @1790:b02dd1e12b3f   11 months markotoplak Added obiDictyMutants to the documentation index.
(edit) @1789:4c7a09867397   11 months marko.toplak Merged biolab/orange-bioinformatics into default
(edit) @1788:ef6b29387bb1   11 months vid.flashpoint Deleted redundant files on the Orange server
(edit) @1787:8caf4af2d6bb   11 months vid.flashpoint Deleted redundant files on the Orange server
(edit) @1786:df95834ddac7   11 months markotoplak obiGeneSetSig: SPCA with threshold selection by permutation.
(edit) @1785:b3a53ba8ada0   11 months markotoplak obiGeneSetSig: added SPCA.
(edit) @1784:6a26e5172130   11 months markotoplak OMIM: uses server files version by default.
(edit) @1783:4a72eace4f4c   11 months markotoplak Register already calls update_server_list internally.
(edit) @1782:e6ed6e7bced3   11 months vid.flashpoint Added Phenotypes to DictyMutants hierarchy
(edit) @1781:764dc2b10839   11 months vid.flashpoint First attempt at configuring Orange server update
(edit) @1780:5cc362d703bb   11 months vid.flashpoint DictyMutants geneset working
(edit) @1779:736a0fc7fccf   11 months vid.flashpoint Merged biolab/orange-bioinformatics into default
(edit) @1778:a94aec22f398   12 months vid.flashpoint Added pickling to, changed the URL in's …
(edit) @1777:ab15a6b6fbbe   12 months vid.flashpoint obiDictyMutants now functional
(edit) @1776:e7da84795108   12 months vid.flashpoint obiDictyMutants now functional
(edit) @1775:023037d1e29a   12 months markotoplak obiGeneSetSig: LLR uses combined standard deviation if a standard …
(edit) @1774:d0585dc25172   12 months markotoplak obiGeneSetSig: added another method based on likelihood ratios by Su et al …
(edit) @1773:5e6e42c393a9   12 months markotoplak Small changes to miRNA update scripts. Added title and tags to elements …
(edit) @1772:58718fc3f736   12 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   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   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.
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