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2017-05-21Merge from the diet branch.Pjotr Prins
* 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
2017-05-16Fixed issue that caused mapping to not work for R/qtlzsloan
Updated dataset menu dropdown info Began adding option to download statistics figures as PNG
2017-04-25Fixed issue with correlation result trait links if target dataset is ↵zsloan
different from base dataset 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
2017-04-17Added option to remove collections from collection list pagezsloan
Improved appearance of search result and collection tables
2017-04-05Added images directory with various gifs, etczsloan
2017-04-05Merge branch 'testing' of github.com:genenetwork/genenetwork2 into developmentzsloan
2017-04-05Merge pull request #251 from lyan6/masterzsloan
Add meta info (X axis, Y axis) for Correlation Scatterplot
2017-04-05- Temporary traits can be created, viewed, and added to collectionszsloan
- 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
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 branch 'testing' of github.com:genenetwork/genenetwork2Lei Yan
2017-03-16Merge /home/zas1024/geneLei Yan
2017-03-16Add meta info (X axis, Y axis) for Correlation ScatterplotLei Yan
2017-02-09Merge pull request #247 from zsloan/masterzsloan
A couple minor commits
2017-02-09Fixed issue where I forgot to add GeneticType to the query_for_group query ↵zsloan
for non-mRNA Assay datasets Increased digits of some Basic Statistics values from 2 to 3
2017-02-09Changed second column header to 'Value' when there's only one sample groupzsloan
2017-02-09Merge pull request #246 from zsloan/masterzsloan
Added genetic_type to DatasetGroup object to differentiate between wh…
2017-02-09Added genetic_type to DatasetGroup object to differentiate between which ↵zsloan
groups should show dominance effect Minor changes/improvements for trait page Updated dataset_menu_structure.json
2017-02-08Merge pull request #245 from zsloan/masterzsloan
Changed the way .fam files are written/read, which fixes the issue wi…
2017-02-08Changed the way .fam files are written/read, which fixes the issue with ↵zsloan
GEMMA mapping accuracy.
2017-02-06Merge pull request #242 from zsloan/masterzsloan
Mapping results figure now correctly says whether GEMMA was used as m…
2017-02-06Mapping results figure now correctly says whether GEMMA was used as mapping ↵zsloan
method.
2017-02-06Merge pull request #241 from zsloan/masterzsloan
Removed reference to trait_submission since it isn't used yet
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 pull request #240 from zsloan/masterzsloan
Various changes
2017-02-06Merge branch 'master' of github.com:zsloan/genenetwork2zsloan
2017-02-06Fixed appearance of several tables (search, mapping results, sample data)zsloan
Temporarily removed second sample table for CFW traits Fixed location of global search bar to work with wider screens
2017-02-02Merge /home/zas1024/geneLei Yan
2017-01-26Merge pull request #237 from zsloan/masterzsloan
Various changes/fixes
2017-01-26Merge pull request #1 from genenetwork/testingzsloan
Various changes/fixes
2017-01-26GEMMA now works with CFW data (had to update where it looks for the input ↵zsloan
files and how it writes the phenotype file) 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
2017-01-03Fixed appearance of samples tables in show_trait to look like all the other ↵zsloan
tables Disabled sorting for the first column (check box) of the samples tables
2016-12-15Merge pull request #234 from zsloan/masterzsloan
Various changes
2016-12-15Changed table appearancezsloan
Updated dataset_menu_structure.json
2016-12-13Fixed a problem related to the last commit that caused a problem when ↵zsloan
loading a collection or doing ctl analysis
2016-12-12Moved a bunch of functions out of the GeneralTrait class that didn't need to ↵zsloan
be there and changed the code that calls them accordingly 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
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 ↵zsloan
sample p 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
2016-11-21Merge pull request #235 from lyan6/masterPjotr Prins
Thanks. Fix sql error: (GeneNetwork error: (_mysql_exceptions.OperationalErro…
2016-11-18Fix sql error: (GeneNetwork error: (_mysql_exceptions.OperationalError) ↵Lei Yan
(1054, "Unknown column 'mouse' in 'where clause'") [SQL: '\n select Geno)
2016-11-15Fixed issue where sample values of 0 would sometimes be displayed as 'x', ↵zsloan
which would result in wrong correlation results Fixed issue where the mean would sometimes be displayed into of the additive effect
2016-11-11Fixed error causing correlation matrix page to not work with 2 traits ↵zsloan
(related to factor loadings table) 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
2016-11-11Fixed problem that caused checkboxes to not work with Scroller search ↵zsloan
results pages Improved the way the table width is set for search results page
2016-11-08READMEPjotr Prins
2016-11-08Merge pull request #232 from DannyArends/testingPjotr Prins
Updates to the CTL analysis
2016-11-08Adding the joss badgeDannyArends
2016-11-08Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingDannyArends
2016-11-07Adding functions addNode and addEdge, to separate out the cytoscape graph ↵DannyArends
creation from the main CTL analysis code
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