source: orange-bioinformatics @ 1839:1a5915cb9665

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(edit) @1839:1a5915cb9665   9 months vid.flashpoint Merged biolab/orange-bioinformatics into default
(edit) @1838:07a55cc13375   9 months vid.flashpoint Added an icon for OWCustomSets.py
(edit) @1837:3ca19c9e0eb2   9 months vid.flashpoint Fixed a filename bug in OWCustomSets.py
(edit) @1836:b14df26ba71c   9 months ales.erjavec Reverted part of changeset 857938f13079 ('load_local' definition …
(edit) @1835:fa00a0fd32a9   10 months vid.flashpoint Fixed the exception handling in obiGeneSets.py
(edit) @1834:91f840200ae3   10 months vid.flashpoint Changed the exception value from KEGG.OrganismNotFound to …
(edit) @1833:4bc95b0f3ef5   10 months vid.flashpoint Added the short name tags in updateGO.py
(edit) @1832:2c6d506ce3f2   10 months vid.flashpoint Added the short name tags in updateGO.py
(edit) @1831:43e5f6912372   10 months vid.flashpoint Added short name tags for GO annotations and NCBI gene info/gen history
(edit) @1830:e965b42c34c6   10 months vid.flashpoint Added short names to miRNA Orange server files
(edit) @1829:fecd89f0776c   10 months vid.flashpoint Changed the labels in miRNA files on the Orange server
(edit) @1828:857938f13079   10 months vid.flashpoint Added an organisms shortname() function to the obiTaxonomy.py to add short …
(edit) @1827:d9c6f60c5632   10 months vid.flashpoint Removed the select/unselect all gene sets check box from …
(edit) @1826:f402285698e5   10 months vid.flashpoint Created the obiGeneAtlasSets.py script, to easily prepare gene sets from …
(edit) @1825:7187e6ba2114   10 months vid.flashpoint Added some missing info to the obiGeneAtlas.py API
(edit) @1824:4c6214cbc159   10 months vid.flashpoint Shortened the p_val display statement in OWSetEnrichment.py
(edit) @1823:fb105c3cd60f   10 months vid.flashpoint Merged biolab/orange-bioinformatics into default
(edit) @1822:8634a5cd44d4   10 months markotoplak Moved custom sets to the main widgets.
(edit) @1821:63ddbd52fdd0   10 months markotoplak Minor changes in widget appearance.
(edit) @1820:8d6175dc404b   10 months vid.flashpoint Fixed the bug of having less than 5 genes in a geneset
(edit) @1819:592576d83807   10 months vid.flashpoint Version 2 of the OWCustomSet.py widget
(edit) @1818:ffa449bd9709   10 months vid.flashpoint Version 1 of the OWCustomSet.py widget
(edit) @1817:157e69dfa030   10 months vid.flashpoint The opened files are now directly imported as custom genesets in …
(edit) @1816:1ddb05ba025a   10 months vid.flashpoint Changed the hierarchy name of Custom gene sets in obiGeneSets.py. Moved …
(edit) @1815:cbaee4a39a94   10 months vid.flashpoint The OWCustomSets.py widget's preview pane has been improved to show a …
(edit) @1814:c7d693f650af   10 months vid.flashpoint Added a genesets statistics function to obiGeneSets.py. Added additional …
(edit) @1813:c4f8bb01af16   10 months vid.flashpoint Removed the .pyc files from the commit
(edit) @1812:6871643ec38f   10 months vid.flashpoint Custom genesets now use Custom Genesets hierarchy in obiGeneSets.py. …
(edit) @1811:d89e4d232162   10 months vid.flashpoint Merged biolab/orange-bioinformatics into default
(edit) @1810:ad758982f7eb   11 months markotoplak Renamed inputs and outputs of gene set enrichment widget.
(edit) @1809:b543c10a4aad   11 months markotoplak Gene set enrichment widget detects gene sets with taxid == None.
(edit) @1808:c80623c809a1   11 months markotoplak OWtest can now appear in canvas.
(edit) @1807:666d56b81a52   11 months vid.flashpoint The OWtest.py prototype widget for custom gene sets now correctly imports …
(edit) @1806:728988337b94   11 months vid.flashpoint The prototype widget for adding and removing custom gene sets
(edit) @1805:c2e4880abd58   11 months vid.flashpoint Added functionality to obiGeneSets.py to remove locally stored gene sets. …
(edit) @1804:4981b5cd8411   10 months ales.erjavec Fixed progress bar initialization (call order) in Gene Set Enrichment.
(edit) @1803:e8183616f755   11 months markotoplak obiGeneSetSig: slow implementation of LLR to test correctness
(edit) @1802:959e64f489d2   11 months markotoplak obiGeneSetSig: Prevent crashing of LLR if the standard deviation is zero.
(edit) @1801:bcc2ac03fb4f   11 months markotoplak obiGeneSetSig: data caches get reset at build_features instead of …
(edit) @1800:017fad842a3e   11 months markotoplak Version bump.
(edit) @1799:2f952a765716   11 months markotoplak Merged changes from Vid's branch.
(edit) @1798:f1e73901a1d3   11 months vid.flashpoint Added Reactome Pathways genesets for humans
(edit) @1797:43f9097a0bc8   11 months vid.flashpoint obiOMIM.py is now correctly updated
(edit) @1796:a8618bd60eb7   11 months vid.flashpoint Merged obiOMIM.py latest commit
(edit) @1795:663192bd4469   11 months vid.flashpoint Removed obiCytobands.py and created genesets in obiGeneSets.py. …
(edit) @1794:3a530b619d7f   11 months vid.flashpoint Added Cytobands genesets and modified obiOMIM.py. 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 obiDictyMutants.py
(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   11 months vid.flashpoint Added pickling to obiDictyMutants.py, changed the URL in obiGeneSets.py's …
(edit) @1777:ab15a6b6fbbe   12 months vid.flashpoint obiDictyMutants now functional
(edit) @1776:e7da84795108   12 months vid.flashpoint obiDictyMutants now functional
(edit) @1775:023037d1e29a   11 months markotoplak obiGeneSetSig: LLR uses combined standard deviation if a standard …
(edit) @1774:d0585dc25172   11 months markotoplak obiGeneSetSig: added another method based on likelihood ratios by Su et al …
(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 obiDictyMutants.py
(edit) @1765:b497b961c944   12 months vid.flashpoint Added obiDictyMutants.py
(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 obiDictyMutants.py
(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 obiKEGG.py 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.
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