genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2016-04-06	The option to switch between LRS and LOD for the GN1 mapping figure should ↵	zsloan
	now work correctly. The correct value (LRS or LOD) will now be displayed in the results table Added glossary links for GN1 mapping figure options (permutations, bootstrap, etc)
2016-04-06	Setting lodm to always be 1.0 fixes the issue where it would incorrectly ↵	zsloan
	display LOD scores for the Y-Axis instead of LRS values
2016-04-06	Permutations (suggestive/significant lines, legend, and histogram) should ↵	zsloan
	now work for both R/qtl and qtl reaper mapping. Changed the logic for receiving permutation/bootstrap info when loading mapping page in different ways (from show_trait, from remapping, from clicking single chromosome) Added text below figure when Allele Effects selected/relevant
2016-04-05	Bootstrap test should now work correctly for qtl reaper mapping method on ↵	zsloan
	full genome view There seems to be some issue with the way it does single chromosome bootstrap tests compared with GN1, though. It seems like GN1 completely re-runs the test for that specific chromosome, while GN2 just takes a subset from the previously calculated bootstraps
2016-04-05	Fixed issue where haplotype analyst option would appear when using ↵	zsloan
	genetic(centimorgan) mapping
2016-03-30	Disabled Haplotype Analyst option if mapping scale is centimorgan/genetic	zsloan

2016-03-30	GN1 mapping now when mapping scale is centimorgan (for R/qtl)	zsloan
	Fixed some issues related to zooming in on chromosome X Fixed problem where it threw an error for mapping methods that didn't return additive effect Fixed problem where the endMb in the top form would be set to the endMb of the last chromosome when viewing full genome
2016-03-29	Additive effect option now works for GN1 mapping figure	zsloan

2016-03-29	Forgot to add GeneralObject file needed for haplotype analyst in last commit	zsloan

2016-03-29	Haplotype Analyst now works for GN1 mapping figure	zsloan
	Chromosome drop-down select and Mb range text fields now are set to the values the user last selected
2016-03-28	Legend option now works for GN1 mapping figure	zsloan

2016-03-28	Trait sample data table width now dynamically changes with number of ↵	zsloan
	attributes and standard error
2016-03-24	Graph width can now be set in Mapping Results	zsloan

2016-03-24	Add the Gene Track option to display the Gene Band for single chromosome view	zsloan
	Fixed an issue where width wasn't being set correctly, so chromosome view is correct width now (was too short before)
2016-03-24	Mapping results table is now limited to the top 200 markers; previously the ↵	zsloan
	page took a long time to load when there were too many markers
2016-03-23	You can now select chromosome and an Mb range from the top menu and remap	zsloan
	The track in the single chromosome view to zoom into smaller intervals now works correctly again
2016-03-23	Fixed GN1 mapping plots so that Y axis and the Y coordinates of manhattan ↵	zsloan
	plot points are correct Table filters markers so it can always be displayed now (previously was too large for GEMMA)
2016-03-21	Manhattan plot option now works for GN1 map, and GEMMA is set to display as ↵	zsloan
	manhattan plot
2016-03-21	Changed code parsing marker csv file to increase GEMMA speed	zsloan
	Currently commenting out the vector map/table for GEMMA since they cause the page to hang, I'll try to figure out a way to prevent this
2016-03-18	Forgot to not retrieve sample data for the phenotype global search with the ↵	zsloan
	last commit, added it now
2016-03-18	Merge branch 'development' of github.com:genenetwork/genenetwork2	zsloan

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