source: orange-bioinformatics @ 1935:0df377c3de76

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Diff Rev Age Author Log Message
(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 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 …
(edit) @1862:49d9912ff84f   6 months markotoplak Version bump
(edit) @1861:d80f56ee144e   6 months markotoplak gene set enrichment widgets corretly uses gene sets without species given
(edit) @1860:504bc511801c   6 months markotoplak obiGeneSets.collections raises an exception if gene sets are not found. …
(edit) @1859:6119125fa435   7 months ales.erjavec Added report.
(edit) @1858:c5c08ee1c3d2   7 months ales.erjavec Added some doc strings.
(edit) @1857:abf1cbef7844   7 months ales.erjavec Added saved selections to the Select Genes widget.
(edit) @1856:3a78a9c860fb   7 months markotoplak Version bump. hG: Enter commit message. Lines beginning with 'HG:' are …
(edit) @1855:b6778baf5104   7 months markotoplak PIPAx: experiment sorting works properly for numbers also.
(edit) @1854:e11c55eccd57   7 months ales.erjavec Fixed input data handling.
(edit) @1853:124130167b7d   7 months ales.erjavec Added inline completion of the common prefix.
(edit) @1852:e470cd151036   7 months ales.erjavec Added an icon for Select Genes widget.
(edit) @1851:aa8ea42e2c8d   7 months ales.erjavec Added an option to order instances by the selected gene names.
(edit) @1850:5b514f87a15e   7 months ales.erjavec Added multi item completion.
(edit) @1849:bd2ced9dddb8   7 months markotoplak Widget rename: Gene selection -> Differential expression
(edit) @1848:8870b3c7cf34   7 months ales.erjavec Remove already entered names from the completion model.
(edit) @1847:b95670287855   7 months ales.erjavec Add a space after the inserted completion.
(edit) @1846:9be60f38b837   7 months ales.erjavec Added 'Select Genes' widget.
(edit) @1845:efe30810466a   8 months markotoplak OWHeatMap: fixed progress bars.
(edit) @1844:9d532651ea3b   8 months markotoplak OWHeatMap: swapped X,Y labels. Fixed progress bar.
(edit) @1843:beaf2389bf47   8 months vid.flashpoint Merged separate calls to hierarchical clustering for x and y into a single …
(edit) @1842:f5f76d0b5ed9   8 months markotoplak Code organization in OWHeatMap.
(edit) @1841:54ca2a1261d7   8 months vid.flashpoint Separated the row and column clustering in
(edit) @1840:66a7f9e0a719   8 months vid.flashpoint Separated the row and column clustering in
(edit) @1839:1a5915cb9665   9 months vid.flashpoint Merged biolab/orange-bioinformatics into default
(edit) @1838:07a55cc13375   9 months vid.flashpoint Added an icon for
(edit) @1837:3ca19c9e0eb2   9 months vid.flashpoint Fixed a filename bug in
(edit) @1836:b14df26ba71c   9 months ales.erjavec Reverted part of changeset 857938f13079 ('load_local' definition …
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