genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
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)
2017-08-23	Update corr scatterplot	Lei Yan

2017-08-03	remove brackets	Lei Yan

2017-08-02	Remove duplicate codes	Lei Yan

2017-08-02	Merge branch 'testing' of github.com:genenetwork/genenetwork2	Lei Yan

2017-08-02	Update Correlation Scatterplot parameters	Lei Yan

2017-07-06	Merge branch 'testing' into developmentdevelopment	zsloan

2017-07-06	Improved table appearance for global searches	zsloan
	Scatterplot Matrix works again Added the first few changes to get covariates working (not done yet)
2017-07-03	Update Statistic table in Correlation Scatterplot	Lei Yan

2017-06-30	Fix Correlation Scatterplot axis format	Lei Yan

2017-06-29	Update Correlation Scatterplot	Lei Yan

2017-06-28	Update Correlation Scatterplot	Lei Yan

2017-06-26	Merge branch 'master' of github.com:genenetwork/genenetwork2	Lei Yan

2017-06-26	Fix Correlation Scatterplot things	Lei Yan

2017-06-14	Changed color scale for heatmap to blue <-> white <-> red	zsloan
	Removed an extraneous character in the gsearch_pheno html
2017-06-14	Removed scatterplot matrix option since it isn't working correctly right now	zsloan
	Removed Download as PNG option for Probability Plot since it also isn't working yet
2017-06-14	Added descriptions for GEMMA and PLINK as well as a warning about the issue ↵	zsloan
	with GEMMA where you can't run it simultaneously on two traits from the same group
2017-06-13	Fixed trait links in network graph nodes	zsloan
	Added warning notifying users that file upload option in the submit_trait page doesn't work yet
2017-06-13	Added to border to table footer in search results	zsloan

2017-06-13	Fixed issue that caused haplotype analyst to no longer work	zsloan
	Fixed Results table for centimorgan results to display cM instead of Mb
2017-06-13	Fixed minor issue where the part of the legend describing the LRS/LOD line ↵	zsloan
	still appeared for manhattan plots
2017-06-12	Merge branch 'development' of github.com:genenetwork/genenetwork2 into ↵	zsloan
	development
2017-06-12	Added explanatory text to heatmap page	zsloan

2017-06-12	Fix binary paths for GEMMA_COMMAND, PYLMM_COMMAND and PLINK_COMMAND	Pjotr Prins

2017-06-12	Fixed issue where 0.0 values would be converted into X's on the trait page	zsloan

2017-06-09	Merge /home/staging/gene into development	zsloan

2017-06-09	- Changed the way the genofile is set so different genofiles can be selected ↵	zsloan
	for mapping - Now shows error page for Correlation Matrix if traits aren't all from the same group (later need to make it check for shared samples, since different groups may contain some of the same samples - Mapping results page now displays the genofile in the information section - Only show Interval Analyst if species is mouse or rat (previously it would show a blank table for other species) - Network Graph now only shows links in a node's info if the relevant information (for example geneid) exists, and the label changes depending on the type of data set - Other minor changes to the appearance of the Network Graph menu (less white space, plus clickable descriptions for a couple options) - Improved Correlations Results page to shorten Description and Authors cell content for Phenotype traits (to keep table width manageable) - Changed the glossary links for LRS and Additive Effect columns for Gene Global Search - Improved appearance for Phenotype Global Search results - Temporarily removed Mapping options/features that don't work from the trait page