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2017-03-06phewas: preparing for use of phewas toolsPjotr Prins
2017-03-05Unused importsPjotr Prins
2017-03-05Settings: make sure paths exist when starting serverPjotr Prins
2017-03-05Merge auwerxPjotr Prins
2017-03-05Merge branch 'master' of github.com:zsloan/genenetwork2 into zsloanPjotr Prins
2017-03-04Creating the EPheWas object in pythonDannyArends
2017-03-04Starting integration of the ePheWas toolDannyArends
2017-03-04Minor update to the commentsDannyArends
2017-02-17Polishing, adding the help at the side, PheWAS integrated fully (untill I ↵DannyArends
can talk to Hao)
2017-02-17Cleaning up the templates, adding the LOC adjusted columnDannyArends
2017-02-17Connecting p.adjust parameters, and updating the region size parameterDannyArends
2017-02-17Template connects to R, userinput handled/passed towards R from the python codeDannyArends
2017-02-16Updated templates to show a table for GN2DannyArends
2017-02-16Phewas output table code in pythonDannyArends
2017-02-10Working PheWAS in GN2, only for chromosome 1 on 25 megabases, but it's a startDannyArends
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
2017-02-09Added 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
2017-02-09Initial code that allows us to run the PheWAS tool, using pre-computed data, ↵DannyArends
still a lot of TODO's left
2017-02-08Changed the way .fam files are written/read, which fixes the issue with ↵zsloan
GEMMA mapping accuracy.
2017-02-08Adding the analysis structure of the PheWAS analysis in the python code, ↵DannyArends
it's all stubs not working and crashing atm
2017-02-08Renamed the analysis code files to include the word analysis to not conflict ↵DannyArends
with the routes in views.py
2017-02-08Deadly Sin #1 changing the javascript without touching the coffeescript ↵DannyArends
which generates this javascript, since we're down the rabbit hole aready I'm just gonna join. CHristian will try n figure out how deep the rabbit hole goes.
2017-02-08Adding routes for all 3 analysis toolsDannyArends
2017-02-08Adding stub display templates for all 3 analysis toolsDannyArends
2017-02-07empty output template to show the results from PheWAS analysisDannyArends
2017-02-07Inital python code to do PheWAS analysis from RDannyArends
2017-02-07Added a new route for the PheWAS resultsDannyArends
2017-02-07Templated html to show the PheWAS analysis input options on the trait pageDannyArends
2017-02-07Adding an initial new trait page for a tabbed pane holding PheWAS, ePheWAS ↵DannyArends
and Mediation
2017-02-07Initial empty file, this will hold the PheWAS tools at a later point in timeDannyArends
2017-02-07Adding a new panel to hold the upcomming PheWAS toolsDannyArends
2017-02-06Mapping results figure now correctly says whether GEMMA was used as mapping ↵zsloan
method.
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)zsloan
Temporarily removed second sample table for CFW traits Fixed location of global search bar to work with wider screens
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
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