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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
2017-02-09Initial code that allows us to run the PheWAS tool, using pre-computed data, ↵DannyArends
still a lot of TODO's left
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
2016-10-07Startup script: add profile to the PATH and set LC_ALL to default to C ↵Pjotr Prins
(should be changed some day)
2016-10-06URLs: replaced non-functioning URLsPjotr Prins
2016-10-06Footer: updating URLsPjotr Prins
2016-10-06Do not open new page in browser on URLPjotr Prins
2016-10-06Removed dead URLPjotr Prins
2016-10-06URL: replaced dead Memphis URL with current GN2 machinePjotr Prins
2016-10-06URL: prevent opening new pagesPjotr Prins
2016-10-06URL: updated Amigo reference on front pagePjotr Prins
2016-10-06URLs: update GO database URL and removed opening new browser pagesPjotr Prins
2016-10-06Logger: add more granular debug messagesPjotr Prins
2016-10-06Merge branch 'master' of github.com:genenetwork/genenetwork2 into mechanizePjotr Prins
2016-10-06CTL requires 2 traits minimally. Also use traits/phenotypes consistentlyPjotr Prins
2016-10-05CTL now displays proper error if fewer than 4 traits are selected. Also, ↵zsloan
WGCNA previously incorrectly gave an error when fewer than 5 traits were selected instead of fewer than 4 (because it said '<= 4'). I also improved the formatting for the html for both CTl and WGCNA Analysis.
2016-10-05Show datasets only on debugPjotr Prins
2016-10-05Minor editPjotr Prins
2016-10-05Reverted on genotype selector on page show_trait_mapping_tools.html - ↵Pjotr Prins
pending the full PR
2016-10-05Tests: Mapping tests pass nowPjotr Prins
2016-10-05print statements should be loggerPjotr Prins
2016-10-05print statements should be loggerPjotr Prins
2016-10-05Testing: show --all optionPjotr Prins
2016-10-05Merge branch 'zsloan' into jsonPjotr Prins
2016-10-05Merge branch 'master' of github.com:zsloan/genenetwork2 into zsloanPjotr Prins
2016-10-05Doc: on testing with Mechanical RobPjotr Prins
2016-10-04Fixed issue that caused adding to existing collections when not logged in to ↵zsloan
not work correctly. The problem was that it would get the collection name from the "new_collection" field instead of the "existing_collections" dropdown.
2016-10-04Merge branch 'master' of github.com:zsloan/genenetwork2 into zsloanPjotr Prins
2016-10-03Merge branch 'master' of github.com:genenetwork/genenetwork2zsloan
2016-10-03Fixed problem that caused R/qtl with permutations to not work correctlyzsloan
2016-10-03Moved rqtl mapping code out of marker_regression and into its own file.zsloan
Later we will want to run all mapping methods outside of the web server, though
2016-10-03Use of GN2_PROFILEPjotr Prins
2016-10-03Config: supporting JSON OVERRIDESPjotr Prins
2016-10-03Debug: sanitize some outputPjotr Prins
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