source: orange-bioinformatics @ 1872:5518b82614e3

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(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 OWHeatMap.py
(edit) @1840:66a7f9e0a719   8 months vid.flashpoint Separated the row and column clustering in OWHeatMap.py
(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   11 months vid.flashpoint The opened files are now directly imported as custom genesets in …
(edit) @1816:1ddb05ba025a   11 months vid.flashpoint Changed the hierarchy name of Custom gene sets in obiGeneSets.py. Moved …
(edit) @1815:cbaee4a39a94   11 months vid.flashpoint The OWCustomSets.py widget's preview pane has been improved to show a …
(edit) @1814:c7d693f650af   11 months vid.flashpoint Added a genesets statistics function to obiGeneSets.py. Added additional …
(edit) @1813:c4f8bb01af16   11 months vid.flashpoint Removed the .pyc files from the commit
(edit) @1812:6871643ec38f   11 months vid.flashpoint Custom genesets now use Custom Genesets hierarchy in obiGeneSets.py. …
(edit) @1811:d89e4d232162   11 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   12 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   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 …
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