genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2018-01-12	Add functions to help handle github login	Muriithi Frederick Muriuki
	* Add functions to help with the github OAuth2 login process
2018-01-12	Add elasticsearch_tools module	Muriithi Frederick Muriuki
	* Collect variables and functions for using the elasticsearch system in a separate module.
2018-01-12	Add client_id and client_secret configurations	Muriithi Frederick Muriuki
	* Provide the OAuth2 client_id and client_secret values in configuration variables.
2018-01-10	Add template elements for OAuth login	Muriithi Frederick Muriuki
	* Add html elements that will be used to prompt users to login with either GitHub or ORCID.
2018-01-10	Add configuration variables for external services	Muriithi Frederick Muriuki
	* Add configuration variables for GitHub and ORCID which will be used by the system to allow users to login.
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)
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