genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2016-03-18	Replaced header with other information in qtl map	zsloan
	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)
2016-03-17	Fixed a bunch of geno files that had most of their contents removed for some ↵	zsloan
	reason
2016-03-15	Merge branch 'development' of github.com:genenetwork/genenetwork2	zsloan

2016-03-15	Merge branch 'master' of github.com:genenetwork/genenetwork2	zsloan

2016-03-15	Merge branch 'master' of github.com:genenetwork/genenetwork2 into development	zsloan

2016-03-15	Merge branch 'master' of https://github.com/genenetwork/genenetwork2	zsloan

2016-03-15	Fixed the mapping figure track that lets you zoom into a smaller range	zsloan
	Fixed the third party mapping figure tracks to refer to the correct chromosome (before it was always 1)
2016-03-15	Added mapping output file directory to gitignore	zsloan

2016-03-14	Changed the way headers look across all pages	zsloan
	Changed the way details are displayed in show trait page Changed search query so that it orders results by symbol
2016-03-03	Fixed issue where correlation would do mapping if run after mapping	zsloan

2016-03-03	Merge branch 'master' of github.com:genenetwork/genenetwork2 into development	zsloan

2016-03-03	Fixed trait export to include SE values	zsloan

2016-03-03	Merge branch 'master' of https://github.com/genenetwork/genenetwork2	zsloan

2016-03-03	Update gsearch.py	Lei Yan

2016-03-02	Increased gsearch speed by removing unnecessary query for sample data	zsloan
	Still slower than preferable due to having to query the gn1 database for every trait in the search results
2016-03-01	Merge branch 'master' of https://github.com/genenetwork/genenetwork2	zsloan

2016-03-01	Committing change to dataset menu before pull	zsloan

2016-03-01	Fixed 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
2016-02-26	PLINK should not run correctly and graph using GN1 image	zsloan
	Updated dataset menu structure json Increased the width for the label and text field for inputting MAF for PLINK and GEMMA
2016-02-25	fixed untracked files	zsloan

2016-02-24	GEMMA mostly working with gn1 mapping, though there may be some issue with ↵	zsloan
	the y scale
2016-02-18	Edited gen_select_dataset to remove confidential datasets	zsloan
	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
2016-02-15	Fixed R/qtl mapping so the group (BXD, etc) isn't hardcoded	zsloan
	Removed an extraneous </td> tag from the show trait page
2016-02-11	Updated jquery validation plugin, now works in IE	zsloan
	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
2016-02-08	Fixed 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)
2016-02-08	Merge branch 'master' of github.com:genenetwork/genenetwork2 into development	zsloan
	Conflicts: .gitignore
2016-02-08	Guix: installation notes	pjotrp

2016-02-08	Renamed misc dir to doc	pjotrp

2016-02-08	Removing LFS	pjotrp

2016-02-08	gitignore: resolved conflict	pjotrp

2016-02-08	Merge branch 'master' of github.com:genenetwork/genenetwork2 into gn-master	pjotrp

2016-02-04	Most 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
2016-01-29	Info button should now work for phenotype and genotype datasets	zsloan

2016-01-27	Merge branch 'master' of github.com:genenetwork/genenetwork2 into development	zsloan

2016-01-27	Added info button to Dataset dropdown on index page	zsloan
	Fixed script that generates dataset dropdown json file to include accession id Fixed dataset link on search results page
2016-01-26	Removed a bunch of files/directories/packages that are no longer used and ↵	zsloan
	some corresponding imports
2016-01-21	MANIFEST: Ignore output data	pjotrp

2016-01-21	Adding html+js+css+img files into MANIFEST	pjotrp

2016-01-19	Adding Python setup.py support	pjotrp

2016-01-15	Cofactor now works with reaper	zsloan

2016-01-14	Regular and single chr views work for qtl reaper now	zsloan
	Single chr now works for R/qtl (didn't before) Merged qtl reaper code into marker_regression.py
2016-01-12	Mapping works for rqtl and centimorgan scale	zsloan

2016-01-06	Single chromosome view now works for mapping page using GN1's image code	zsloan
	Removed loading bar that appeared on show trait page since it didn't work with GN1 mapping (which opens in a new page)
2016-01-04	Added headers/foots/css to mapping page	zsloan
	Mapping results table now works
2015-12-18	Mapping results open in new window; still need to add header/footer/js	zsloan

2015-12-18	Added image map for figure	zsloan

2015-12-15	Added the js_data so both the GN1 and GN2 figures can be displayed	zsloan

2015-12-14	GN1 mapping full genome figure now correct for pylmm and output to web page	zsloan

2015-12-12	Changed loop drawing qtl curve to fix some issues; still need to make it ↵	zsloan
	draw to different chr areas though
2015-12-09	Disabled GN1 mapping for master branch; mistakenly pushed with it enabled before	zsloan