genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2018-03-29	Fixed box plots and got them to update with changed sample data	zsloan
	Removed fast correlation option because it doesn't work well with gunicorn Changed the type of logger from error to debug when logging which page is being visited in views.py
2018-03-16	Just undoing tabulator changes so I can push other changes	zsloan

2018-03-15	Changed appearance of mapping and correlation options on trait page	zsloan
	Fixed issue where changed sample values were not passed to qtlreaper mapping ("Interval Mapping") Loading factors and their plot are hidden in situations where there's some error with calculating principal components Added GEMMA description and changed order of descriptions for mapping options on trait page
2018-03-02	Added option to display selected covariates for GEMMA mapping	zsloan
	Changed layout/appearance of mapping options Partially fixed issue with deleting collections Changes to correlation table still in progress; having trouble getting tabulator to load JSON
2018-02-26	Merge /home/lei/gene into testing	zsloan

2018-02-26	Committing some in-progress changes related to loading correlation page from ↵	zsloan
	JSON
2018-02-23	update corr scatterplot interface	Lei Yan

2018-02-14	Added empty collection error page to git, since it wasn't on production	zsloan

2018-02-13	Resolved conflict	zsloan

2018-02-13	Just committing very minor change to correlation table so I can pull other ↵	zsloan
	changes
2018-02-13	@zsloan: we should introduce full parameter checking and sensible defaults ↵	Pjotr Prins
	for every page we work on. It will help bug tracking. Probably fixes #279
2018-02-12	Changed code parsing GEMMA output to fix issue where it wasn't getting the ↵	zsloan
	correct p-values
2018-02-12	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing	zsloan

2018-02-12	Quick parallel correlation should work, though I'm not sure why the code ↵	zsloan
	suddenly decided to start running it when it wasn't in the past. Switched correlation table to tabulator
2018-02-10	Fixing GEMMA LOCO	Pjotr Prins

2018-02-10	Fixed finding PATHs - one return statement!	Pjotr Prins

2018-02-10	Check for bimbam path and bail out if it is missing	Pjotr Prins

2018-01-30	gunicorn dev and prod modes added	Pjotr Prins

2018-01-29	Gunicorn works	Pjotr Prins

2018-01-29	startup script: adapting for gunicorn	Pjotr Prins

2018-01-24	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing	zsloan

2018-01-24	Added links for markers in mapping results table when genotypes exist in DB	zsloan
	Added more info to trait details for phenotype traits Changed order of mapping methods Fixed layout of mapping loading screen to hopefully be centered on different screen sizes Improved layout of some elements in mapping results page
2018-01-04	Merge pull request #270 from pjotrp/testing	zsloan
	Merge some older commits
2017-12-20	Added submit_bnw even though it isn't working yet, just so views.py doesn't ↵	zsloan
	throw an error
2017-12-20	Fixed issue that caused Mb ticks to get out of alignment for mapping figure	zsloan

2017-12-20	Fixed the way PLINK outputs phenotype files (though there's still some ↵	zsloan
	problem preventing it from working) Added some code related to new plotly probability plot, though it's commented out until it looks how I want it to Added some code for adding the BNW link to GN2, though it's not working yet Updated dataset menu structure JSON file
2017-12-20	tools: find path for JS and gemma_wrapper	Pjotr Prins

2017-12-20	Bring in some earlier work - mostly documentation and startup handling	Pjotr Prins

2017-12-06	Fixed drop-down group order	zsloan

2017-12-04	Fixed drop-down scripts to more appropriately deal with BXD300 groups ↵	zsloan
	(though there's still a minor issue with a few datasets) Added some header data to mapping output file Fixed links in Network Group nodes/edges
2017-11-22	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing	zsloan

2017-11-22	Added option to export csv of full mapping results	zsloan

2017-11-21	Merge pull request #258 from lyan6/master	zsloan
	improved scatter plots
2017-11-17	Fixed issue that caused GEMMA LOCO to not work on production	zsloan

2017-11-06	Replaced Histogram and Bar Chart with Plotly version and added new Box Plot ↵	zsloan
	with Plotly GEMMA now has option to select genotypes Updated dataset select dropdowns to be ordered correctly Fixed dataset select dropdowns for correlations to not show confidential datasets Added Skewness and Kurtosis to Basic Statistics table Fixed Verify and RNA-seq buttons on trait page Temporarily hardcoded Reference page until we get it to link with database
2017-10-02	Merge branch 'testing' of github.com:genenetwork/genenetwork2	Lei Yan

2017-10-02	save as svg button work	Lei Yan

2017-09-22	Fixed issue that caused covariates to not work for certain data set groups	zsloan

2017-09-22	Fixed issue that caused LOCO to not work when remapping or using single ↵	zsloan
	chromosome view
2017-09-21	LOCO should work with GEMMA (when BIMBAM available), though I still need to ↵	zsloan
	do more testing
2017-09-14	Committing current progress towards implementing LOCO for GEMMA, not done yet	zsloan

2017-09-13	update Correlation Scatterplot format	Lei Yan

2017-09-12	Merge branch 'testing' of github.com:genenetwork/genenetwork2	Lei Yan

2017-09-12	change corr_scatterplot precision format	Lei Yan

2017-09-07	Updated show trait page to correctly show GEMMA options for certain data sets	zsloan

2017-09-07	Added the script to convert bimbam to kinship matrices	zsloan

2017-09-05	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing	zsloan

2017-09-05	Added file converting genofiles to bimbam	zsloan

2017-09-04	gemma-wrapper: find binary in profile	Pjotr Prins

2017-08-29	Mostly changes related to getting gemma working with covariates and BIMBAM ↵	zsloan
	file format Other changes include: - Fixing links in the network graph - Changing button colors on show trait page - Changing color scheme for heatmap - Making rows highlight in yellow when clicked on - Some changes to table appearance (like giving gene global search a horizontal scroll)