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2017-05-31Added various tool options to correlation results page and improved table app......Fixed minor logic issue in trait.py zsloan
2017-05-22Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2017-05-22Added submit trait to header menu and fixed some minor issues with Network Gr...zsloan
2017-05-21Merge from the diet branch.... * refactored ./bin/genenetwork2 and /etc/default_settings - better detection of Guix - removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS - removing some default settings, such as PYLMM_COMMAND - rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY - added GUIX_JS_PATH for JS modules * Added documentation on installing binary GN2 * Updated Twitter board to latest version in Guix - it had broken * Updated many tools in the latest Guix profile Pjotr Prins
2017-05-16Fixed issue that caused mapping to not work for R/qtl...Updated dataset menu dropdown info Began adding option to download statistics figures as PNG zsloan
2017-04-25Fixed issue with correlation result trait links if target dataset is differen......Improved collection list and view table appearances Added question mark image for glossary entries in table headers Fixed issue where extra decimal place sometimes appeared in bar chart Y axis tick values zsloan
2017-04-17Added option to remove collections from collection list page...Improved appearance of search result and collection tables zsloan
2017-04-05Added images directory with various gifs, etczsloan
2017-04-05Merge branch 'testing' of github.com:genenetwork/genenetwork2 into developmentzsloan
2017-04-05- Temporary traits can be created, viewed, and added to collections...- Correct PCA trait data is created but can't be saved yet - Added inner margins by increasing xDomain and yDomain of probability plot on trait page - Increased X/Y-axis label font size - Turned "processes" to 0 on runserver.py for PROD setting, since it doesn't work with threading - Improved appearance of correlation page table - Added links to github to index page - Removed js_data from GEMMA/PLINK mapping results, since it isn't used for those - Removed "Tissue" from trait page for phenotype traits zsloan
2017-04-04Change scatterplot image buffer/innerLei Yan
2017-04-04align X and Y meta infoLei Yan
2017-03-30Change "Correlation Scatterplot" size, font, color, etc.Lei Yan
2017-03-16Merge /home/zas1024/geneLei Yan
2017-03-16Add meta info (X axis, Y axis) for Correlation ScatterplotLei Yan
2017-02-09Fixed issue where I forgot to add GeneticType to the query_for_group query fo......Increased digits of some Basic Statistics values from 2 to 3 zsloan
2017-02-09Changed second column header to 'Value' when there's only one sample groupzsloan
2017-02-09Added genetic_type to DatasetGroup object to differentiate between which grou......Minor changes/improvements for trait page Updated dataset_menu_structure.json zsloan
2017-02-08Changed the way .fam files are written/read, which fixes the issue with GEMMA...zsloan
2017-02-06Mapping results figure now correctly says whether GEMMA was used as mapping m...zsloan
2017-02-06Merge branch 'development' of github.com:zsloan/genenetwork2zsloan
2017-02-06Commented out reference to trait_submission since it's not used yetzsloan
2017-02-06Merge branch 'master' of github.com:zsloan/genenetwork2zsloan
2017-02-06Fixed appearance of several tables (search, mapping results, sample data)...Temporarily removed second sample table for CFW traits Fixed location of global search bar to work with wider screens zsloan
2017-02-02Merge /home/zas1024/geneLei Yan
2017-01-26Merge pull request #1 from genenetwork/testing...Various changes/fixeszsloan
2017-01-26GEMMA now works with CFW data (had to update where it looks for the input fil......Y-axis for GEMMA now says -log(p) Updated the style of the trait sample data table in the trait page Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs) Updated dataset menu json file Added option to show and hide columns to regular search page using colVis Changed regular and global search result table styles/column widths Began work on user trait submission code (not working yet though) Began work on static loading page for mapping results zsloan
2017-01-03Fixed appearance of samples tables in show_trait to look like all the other t......Disabled sorting for the first column (check box) of the samples tables zsloan
2016-12-15Merge pull request #234 from zsloan/master...Various changeszsloan
2016-12-15Changed table appearance...Updated dataset_menu_structure.json zsloan
2016-12-13Fixed a problem related to the last commit that caused a problem when loading...zsloan
2016-12-12Moved a bunch of functions out of the GeneralTrait class that didn't need to ......Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static) Removed some unused code from show_trait.py changed appearance of table headers some, though needs a little more work Updated dataset_menu_structure.json zsloan
2016-11-29Fixed loadings plot so it looks like the GN1 figurezsloan
2016-11-21Fixed correlation page so it correctly sorts by the scientific notation for s......Set default sort for correlation page to sample p Improved appearance of correlation matrix some by decreasing line height Added labels to each figure/table on the correlation page zsloan
2016-11-18Fix sql error: (GeneNetwork error: (_mysql_exceptions.OperationalError) (1054...Lei Yan
2016-11-15Fixed issue where sample values of 0 would sometimes be displayed as 'x', whi......Fixed issue where the mean would sometimes be displayed into of the additive effect zsloan
2016-11-11Fixed error causing correlation matrix page to not work with 2 traits (relate......Also improved factor loads table to show only two factors when there are two traits Fixed error related to get_traits_from_collections.js being called in collections/list before jquery is defined zsloan
2016-11-11Fixed problem that caused checkboxes to not work with Scroller search results......Improved the way the table width is set for search results page zsloan
2016-11-08Adding the joss badgeDannyArends
2016-11-07Adding functions addNode and addEdge, to separate out the cytoscape graph cre...DannyArends
2016-11-07Adding the reference to the paper, and updating the output to show the cytosc...DannyArends
2016-11-07Adding code to the ctl analysis file to output nodes and edges for cytoscapeDannyArends
2016-11-07Javascript file (based on the correlation file) to dsplay CTL networks using ...DannyArends
2016-11-02Fixed typos causing genofile selector to not show up in mapping optionszsloan
2016-11-02Added toggleable short and long labels to correlation matrix...Fixed issue where I forgot to remove a parameter from jsonable_table_row in trait.py zsloan
2016-11-02Merge branch 'testing' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-11-02Added Scroller functionality to regular (but not global) search, which increa......In order to implement Scroller (and make table look nicer), all rows are the same height and excess description/authors text is shown in a tooltip Increased table width for non-Geno DBs Fixed issue where Genotype traits did not fetch their location_repr (text for displaying location), causing that column to be blank in searches Fixed issue causing Correlation Matrix cells to not be colored corresponding with their correlation and also increased cell font a little Fixed issue where dataset link in the Correlation Page did not correctly point to corresponding GN1 page zsloan
2016-10-31Merge branch 'lyan' into testingPjotr Prins
2016-10-31Use existing GENODIR - the metadata can be stored there, next to the....geno files. Pjotr Prins
2016-10-31Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingPjotr Prins
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