source: orange-bioinformatics @ 1962:d35f315a7d08

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Diff Rev Age Author Log Message
(edit) @1962:d35f315a7d08   2 months markotoplak Moved obiExpression -> utils.expression. Removed dependencies on old Gary …
(edit) @1961:3cffa0f0cf0e   2 months markotoplak Remove dependencies for stats in obiGeneSetSig.
(edit) @1960:eb3b4e9bbb4c   2 months markotoplak obiProb backward compatibility.
(edit) @1959:5fb1e8afe0fa   2 months markotoplak Moved obiProb -> utils.stats.
(edit) @1958:42eb39d0cf73   2 months markotoplak obiGEO and obiGene for backward compatibility.
(edit) @1957:a1ac47c53c43   2 months markotoplak Renamed obiGene and obiGEO.
(edit) @1956:4504c102a4bb   2 months markotoplak Version bump.
(edit) @1955:9b187b15f253   2 months markotoplak obiGeneSetSig: pca refactor.
(edit) @1954:9884f85531a9   3 months markotoplak Updated GSEA examples to the new namespace.
(edit) @1953:e1d43f404196   3 months markotoplak Allow organism names (mapped through obiTaxonomy) as species id.
(edit) @1952:db7cc518cd3d   3 months markotoplak Remove obiAssess (superceeded by obiGeneSetSig).
(edit) @1951:0d18fa2df3a9   3 months markotoplak Merge.
(edit) @1950:38e8e32e50a3   3 months markotoplak Add all scripts to the updater.
(edit) @1949:13578f97436a   3 months markotoplak OWPIPAx: avoid eval on older Python.
(edit) @1948:09fcb288b061   3 months markotoplak PIPAx widget can now handle experiments with only some result types.
(edit) @1947:29931e1c32be   3 months ales.erjavec Fixed Gene Info report.
(edit) @1946:70b5918b6184   3 months ales.erjavec Added gene count column to Import Gene Sets dialog.
(edit) @1945:639f70df6b39   3 months markotoplak Temporary fix in Select Genes.
(edit) @1944:91a972497fcc   3 months markotoplak GEO datasets: when outputting samples as rows and there a multiple types, …
(edit) @1943:1eb86966ee38   4 months anze.staric Bump version to 2.5.21. Changed format from 2.5a?? to 2.5.?? because …
(edit) @1942:8fd077fd97ff   4 months ales.erjavec Use 'uniformRowHeights' tree view property for faster layout.
(edit) @1941:42a5e7765fd4   4 months markotoplak Convert obiOMIM documentation to rst.
(edit) @1940:0b3c285adedb   4 months markotoplak Removed obsolete examples.
(edit) @1939:c62fe1ffef7d   4 months markotoplak Remove reference that was converted into rst.
(edit) @1938:7e1dc12fd41e   4 months markotoplak Converted obiGEO documentation to rst.
(edit) @1937:236efba83ca2   4 months markotoplak obiGEO documentation: partial commit.
(edit) @1936:847a781b8798   4 months markotoplak obiGEO documentation: partial conversion to rst.
(edit) @1935:0df377c3de76   4 months markotoplak Version bump, changed documentation URL.
(edit) @1934:d0e896ee439a   4 months markotoplak Converted obiProb documentation to rst.
(edit) @1933:bf2cdd778fee   4 months markotoplak Converted documentation of obiGeneSets to rst.
(edit) @1932:7b87ecd92e85   4 months markotoplak Gene matching documentation.
(edit) @1931:e58b01520933   4 months markotoplak obiKEGG: added pathway search by genes.
(edit) @1930:4a6f881e13d1   4 months ales.erjavec Fixed organism initialization.
(edit) @1929:7f7a315dd9ca   4 months ales.erjavec Store the selected organism as a string (taxid).
(edit) @1928:ef73516807fb   4 months ales.erjavec Threaded initialization and record retrieval.
(edit) @1927:f3f90e6b14dc   5 months ales.erjavec Optimize the case where the organism identifier is a known common taxid.
(edit) @1926:f8dfe8b6d33c   5 months ales.erjavec Update the gene info when the list of organisms becomes available.
(edit) @1925:7c31d7eb40ec   5 months ales.erjavec Added "Import from text file" action.
(edit) @1924:67818b3f5691   5 months ales.erjavec Fix in obiTaxonomy.to_taxid (check if argument is already a valid taxid).
(edit) @1923:f097c4683c3d   5 months ales.erjavec Fixed an AttributeError (uninitialized 'currentAnnotatedCategories' …
(edit) @1922:3c4b5ab67b84   5 months ales.erjavec Ignore wheel events in organism combo box.
(edit) @1921:ac450b5faf1f   5 months ales.erjavec Changed tooltip set labels.
(edit) @1920:16fbbd5ec146   5 months ales.erjavec Implemented completion on gene symbol names.
(edit) @1919:8de40fbc5a87   5 months blaz.zupan Some revision of rst documentation.
(edit) @1918:0e7a2add2967   5 months ales.erjavec Fixed a UnicodeDecodeError when sorting a mixed str/unicode list.
(edit) @1917:fc231a027d1b   5 months ales.erjavec Prettier expanded variable names.
(edit) @1916:bbef37dc8a3e   5 months ales.erjavec Horizontal output table merge.
(edit) @1915:bd88de8d8614   5 months ales.erjavec Changed displayed text labels.
(edit) @1914:f4c8559dd359   5 months ales.erjavec Fixed an error when the input data set does not have any suitable …
(edit) @1913:5e94e30690e0   5 months ales.erjavec Added gene name/description to the completion popup view.
(edit) @1912:83600a89de4c   5 months ales.erjavec Fixed an error on widget input disconnect. The 'data_hints.get_hint' …
(edit) @1911:ff8c04a73827   5 months ales.erjavec Download and load the gene sets in a background thread.
(edit) @1910:98d41e5e04b0   5 months ales.erjavec Fixed organism selection.
(edit) @1909:45044fae44b2   5 months ales.erjavec Added "Import names from gene sets" dialog.
(edit) @1908:a5404b514061   5 months ales.erjavec Interface cleanup, minor parsing speedup.
(edit) @1907:9b35fd5ebae0   5 months ales.erjavec Fixed obo tag value parsing.
(edit) @1906:d3362d98e93d   5 months ales.erjavec Move extra conflicting class variables to meta attributes.
(edit) @1905:389c619d8e5e   5 months ales.erjavec Ignore conflicting class variables in the selected subsets.
(edit) @1904:e999c567f146   5 months ales.erjavec Fixed an error when removing widget inputs.
(edit) @1903:d186587ac38e   5 months ales.erjavec Chaged the selected item's brush pattern.
(edit) @1902:a909124bd644   5 months ales.erjavec Save/restore changed input set titles and selected attributes.
(edit) @1901:3b54fcf76ce2   5 months ales.erjavec Implemented support for editing the set titles.
(edit) @1900:c035c8b79a5a   5 months ales.erjavec Added a 'Venn Diagram' widget.
(edit) @1899:4b3e09f29d19   5 months markotoplak OWSetEnrichment: Fixed loading of selected gene sets. Fixes #1338
(edit) @1898:ce804448cf39   5 months markotoplak Fixed selection of the cell borders in OWHeatMap. Fixes #1336
(edit) @1897:2e74f7146dac   6 months markotoplak Removed PIPA widget, renamed Genotype distances.
(edit) @1896:af1bac66b72c   6 months ales.erjavec Pass 'namespace_packages' parameter to setup function.
(edit) @1895:d242c01f40a3   6 months ales.erjavec Fixed a typo.
(edit) @1894:0c980fd08a69   6 months ales.erjavec Changed Gene Info widget initialization.
(edit) @1893:35769c9c9490   6 months ales.erjavec Added caching of name lookups in obiTaxonomy.
(edit) @1892:5c6f87657211   6 months ales.erjavec Replaced use of safe_text with xml.sax.saxutils.escape
(edit) @1891:d00fa52ab984   6 months markotoplak version bump
(edit) @1890:043f2b1864cd   6 months markotoplak Numberically stable p-values for obiProb.Binomial.
(edit) @1889:2ff9da5aed53   6 months markotoplak Attributes m and n in Hypergeometric test can now be swapped and results …
(edit) @1888:cad892644786   6 months ales.erjavec Changed progress bar updates. The update in the loop was actually slowing …
(edit) @1887:b0dce8ef683c   6 months ales.erjavec Fixes for obiGeneAtlas.
(edit) @1886:5a859e2c6ae1   6 months ales.erjavec Fixes for Arary Express query response parsing.
(edit) @1885:8d4623044732   6 months ales.erjavec Fixes for Array Express caching.
(edit) @1884:bbd363ba9498   6 months ales.erjavec Added option to copy/append the names from "Gene Subset" input to saved …
(edit) @1883:8d992429535b   6 months markotoplak GO widget shows p-value and FDR separately.
(edit) @1882:5f55ddc19cea   6 months ales.erjavec Added an option to select genes in a secondary data table input.
(edit) @1881:eca3f6d25d7d   6 months ales.erjavec Fixed dicty express server url used by the widget.
(edit) @1880:eb9b49b83a02   6 months markotoplak version bump
(edit) @1879:3e9c962d89f8   6 months marko.toplak Merged in ales_erjavec/orange-bioinformatics (pull request #2) Move …
(edit) @1878:8b1e95b04793   6 months ales.erjavec Merged biolab/orange-bioinformatics into default
(edit) @1877:2a17616eb737   6 months ales.erjavec Merged biolab/orange-bioinformatics into default Fixed conflicts in …
(edit) @1876:98f567fbb6f9   6 months ales.erjavec Made orangecontrib.bio into a namespace package.
(edit) @1875:6d87bc9aaf5a   6 months ales.erjavec Cache entry should be invalid if unpickling raises an error.
(edit) @1874:b3e32cc5cf6f   6 months ales.erjavec Added new style widget meta descriptions.
(edit) @1873:0810c5708cc5   6 months ales.erjavec Moved '_bioinformatics' into orangecontrib namespace.
(edit) @1872:5518b82614e3   6 months markotoplak OWSetEnrichment: both p-value and FDR are shown. FDR is recomputed when …
(edit) @1871:aa8b068bd7a1   6 months markotoplak Fixed HeatMap selections with "Sort genes" option. Selection also works …
(edit) @1870:8993be909b62   6 months markotoplak merge
(edit) @1869:b0f2e93c6cd2   6 months markotoplak version bump
(edit) @1868:653b6f191d7d   6 months markotoplak Version bump.
(edit) @1867:e75d81c7f764   6 months markotoplak OWHeatMap: selection hack
(edit) @1866:edd23f3b40fd   6 months markotoplak version bump
(edit) @1865:36118db29ef6   6 months markotoplak Removed changes to OWHeatMap that were commited by accident.
(edit) @1864:0df93c7f4681   6 months markotoplak version bump
(edit) @1863:5b02c518e073   6 months markotoplak Gene Set Enrichment widget: refresh available gene set when species is …
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