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2016-03-18Forgot to not retrieve sample data for the phenotype global search with the ↵zsloan
last commit, added it now
2016-03-18Merge branch 'development' of github.com:genenetwork/genenetwork2zsloan
2016-03-18Replaced header with other information in qtl mapzsloan
Began adding menu to qtl map Fixed global search to not retrieve samples (to increase speed) Got the vector plot working again so it can be displayed alongside the gn1-style plot Only display the vector plot when doing GEMMA to speed up (this might not be necessary)
2016-03-17Fixed a bunch of geno files that had most of their contents removed for some ↵zsloan
reason
2016-03-15Merge branch 'development' of github.com:genenetwork/genenetwork2zsloan
2016-03-15Merge branch 'master' of github.com:genenetwork/genenetwork2zsloan
2016-03-15Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-03-15Merge branch 'master' of https://github.com/genenetwork/genenetwork2zsloan
2016-03-15Fixed the mapping figure track that lets you zoom into a smaller rangezsloan
Fixed the third party mapping figure tracks to refer to the correct chromosome (before it was always 1)
2016-03-15Added mapping output file directory to gitignorezsloan
2016-03-14Changed the way headers look across all pageszsloan
Changed the way details are displayed in show trait page Changed search query so that it orders results by symbol
2016-03-03Fixed issue where correlation would do mapping if run after mappingzsloan
2016-03-03Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-03-03Fixed trait export to include SE valueszsloan
2016-03-03Merge branch 'master' of https://github.com/genenetwork/genenetwork2zsloan
2016-03-03Update gsearch.pyLei Yan
2016-03-02Increased gsearch speed by removing unnecessary query for sample datazsloan
Still slower than preferable due to having to query the gn1 database for every trait in the search results
2016-03-01Merge branch 'master' of https://github.com/genenetwork/genenetwork2zsloan
2016-03-01Committing change to dataset menu before pullzsloan
2016-03-01Fixed csv download and removed non-working "Download Table" button for ↵zsloan
collections list, collection view, gene/pheno global search, and regular search Not sure what the best way to determine the filename is, so just using "search_results" or "collection_list" for now In future I want to replace the default csv download button by attaching its function to the previous "Download Table" button
2016-02-26PLINK should not run correctly and graph using GN1 imagezsloan
Updated dataset menu structure json Increased the width for the label and text field for inputting MAF for PLINK and GEMMA
2016-02-25fixed untracked fileszsloan
2016-02-24GEMMA mostly working with gn1 mapping, though there may be some issue with ↵zsloan
the y scale
2016-02-18Edited gen_select_dataset to remove confidential datasetszsloan
Also hard-coded the removal of Macaque Monkey since I couldn't think of a good way to retroactively check if every dataset in a species is confidential
2016-02-15Fixed R/qtl mapping so the group (BXD, etc) isn't hardcodedzsloan
Removed an extraneous </td> tag from the show trait page
2016-02-11Updated jquery validation plugin, now works in IEzsloan
Fixed a couple minor html syntax erors in login_user.html and base.html Changed export button on correlation page to csvHtml5, but still has problem with commas in fields being interpreted as a new column
2016-02-08Fixed the logic if how the correlation page applies filters (mean ↵zsloan
expression, location, etc) Added back some colorbox directories that we apparently need (I had removed them in an earlier commit)
2016-02-08Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
Conflicts: .gitignore
2016-02-08Guix: installation notespjotrp
2016-02-08Renamed misc dir to docpjotrp
2016-02-08Removing LFSpjotrp
2016-02-08gitignore: resolved conflictpjotrp
2016-02-08Merge branch 'master' of github.com:genenetwork/genenetwork2 into gn-masterpjotrp
2016-02-04Most importantly, this commit fixes an issue that caused the trait page to ↵zsloan
not work because of the new dataset_menu_structure.json file An Intro section is also added to the header, though for the time being its contents aren't populated and the edit option isn't working
2016-01-29Info button should now work for phenotype and genotype datasetszsloan
2016-01-27Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-01-27Added info button to Dataset dropdown on index pagezsloan
Fixed script that generates dataset dropdown json file to include accession id Fixed dataset link on search results page
2016-01-26Removed a bunch of files/directories/packages that are no longer used and ↵zsloan
some corresponding imports
2016-01-21MANIFEST: Ignore output datapjotrp
2016-01-21Adding html+js+css+img files into MANIFESTpjotrp
2016-01-19Adding Python setup.py supportpjotrp
2016-01-15Cofactor now works with reaperzsloan
2016-01-14Regular and single chr views work for qtl reaper nowzsloan
Single chr now works for R/qtl (didn't before) Merged qtl reaper code into marker_regression.py
2016-01-12Mapping works for rqtl and centimorgan scalezsloan
2016-01-06Single chromosome view now works for mapping page using GN1's image codezsloan
Removed loading bar that appeared on show trait page since it didn't work with GN1 mapping (which opens in a new page)
2016-01-04Added headers/foots/css to mapping pagezsloan
Mapping results table now works
2015-12-18Mapping results open in new window; still need to add header/footer/jszsloan
2015-12-18Added image map for figurezsloan
2015-12-15Added the js_data so both the GN1 and GN2 figures can be displayedzsloan
2015-12-14GN1 mapping full genome figure now correct for pylmm and output to web pagezsloan
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