genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2016-05-27	Fixed issue where the Non-BXD (or whatever group/inbred set) table would ↵	zsloan
	show up when there should be no such samples Fixed Interquartile Range link in basic statistics table
2016-05-27	Improved appearance of p values below slider in correlation menu on trait ↵	zsloan
	page. The way I did it is really awful (a bunch of  's) but nothing else seemed to work, including putting a div or span with a fixed width between them
2016-05-26	Merge branch 'master' of github.com:genenetwork/genenetwork2 into development	zsloan

2016-05-26	Merge branch 'master' of github.com:genenetwork/genenetwork2 into development	zsloan

2016-05-26	Merge branch 'master' of https://github.com/genenetwork/genenetwork2	zsloan

2016-05-26	Issue with certain samples (like BXD65a, ones were there are multiple for a ↵	zsloan
	single BXD or whatever) should be fixed for different mapping methods and data set types Renamed directories with genotypes so tools.py didn't need to be changed (which might mess up other deployments) Fixed error when searching genotype data sets
2016-05-23	Reaper mapping results are now correct and account for samples with two ↵	zsloan
	names (like BXD65a) R/qtl and PYLMM still not working with the change and bootstrap results are also still wrong, so need to fix those issues.
2016-05-18	Merge branch 'staging' of https://github.com/genenetwork/genenetwork2	zsloan

2016-05-18	Updated dataset selection dropdown menus and fixed error caused by traits ↵	zsloan
	with no description
2016-05-17	Merge branch 'staging' of github.com:genenetwork/genenetwork2 into development	zsloan

2016-05-17	Merge branch 'staging' of github.com:genenetwork/genenetwork2	zsloan

2016-05-17	Correlations are now much faster after I disabled fetching the sample data ↵	zsloan
	for each result trait
2016-05-13	Fixed path for IM bar plot	Pjotr Prins

2016-05-13	Removing ref. to HTMLPATH	Pjotr Prins

2016-05-13	WebqtlConfig.py: Constant handling	Pjotr Prins

2016-05-13	Fix paths for images	Pjotr Prins

2016-05-10	Correlation successfully uses materialized views and parallel processing, ↵	zsloan
	but for some reason is taking an immense amount of time so need to troubleshoot that Changed order of mapping options to display Interval Mapping first Changed some links to no longer open in new tab/window
2016-05-10	Merge branch 'master' of github.com:genenetwork/genenetwork2 into merge_zach	Pjotr Prins

2016-04-29	Fixed database link in trait page details	zsloan

2016-04-29	Also fixed links in statistics section (for normal probability plot) and ↵	zsloan
	removed 'target=_blank's
2016-04-29	Fixed links in correlation descriptions on trait page and removed ↵	zsloan
	target=_blank (so will not open in new window unless user specifies) Fixed javascript so description changes when user changes the method and "Type" option is removed for literature correlation
2016-04-29	URL: removed _blank from first URL	Pjotr Prins

2016-04-29	Updated mailing list URL	Pjotr Prins

2016-04-29	Plotting: using cairo-png for headless environments	Pjotr Prins

2016-04-29	Merge	Pjotr Prins

2016-04-28	Added option to export permutation results for mapping page	zsloan
	Added data_scale to dataset objects and basic stats table will now check data scale when calculating range Made interval analyst results table work with datatables Changed the appearance of the basic stats table some by giving it a border
2016-04-28	Changed the defunct GeneRIF URL to a working Wikipedia URL (which	Pjotr Prins
	also points to the non-working NCBI link)
2016-04-26	Interval mapping: fix font and image path	Pjotr Prins

2016-04-26	Merging with Zach's latest branch	Pjotr Prins

2016-04-25	Interval Analyst table mostly working, just need to work out a few more things	zsloan

2016-04-22	Fixed issue where manhattan plot setting wasn't being carried over to single ↵	zsloan
	chromosome view for mapping results Removed a useless "if 1 == 1" line that was in marker_regression_gn1.py for testing.
2016-04-20	Interval Mapping now correctly does interval mapping if Marker Regression ↵	zsloan
	isn't checked (it used to just "connect the dots" of the marker regression output) Changed "Manhattan Plot" label to "Marker Regr." to accurately reflect what the option does
2016-04-20	Added borders to stats table in trait page	zsloan

2016-04-20	Fix typo	Pjotr Prins

2016-04-20	A few fixes to get the webserver running again	Pjotr Prins

2016-04-20	Add file	Pjotr Prins

2016-04-20	trasnform to transform	DannyArends

2016-04-20	Changed the file stem of generated pictures to CTL	DannyArends

2016-04-20	Adding small figures per trait, so that users can see CTL and QTL for each ↵	DannyArends
	individual phenotype
2016-04-20	Adding parameters, and passing them to the CTL algorithm	DannyArends

2016-04-20	Working on the output template of CTL	DannyArends

2016-04-20	Updates to the CTL code adding the significant results to the result object	DannyArends

2016-04-20	Cleaning code, adding comments	DannyArends

2016-04-20	Adding the lineplot image to the output	DannyArends

2016-04-20	Adding code to do initial CTL mapping (working on the BXD)	DannyArends

2016-04-20	Parsing the names of the individuals, and coding H as -999	DannyArends

2016-04-20	Minor changes to the CTL setup template	DannyArends

2016-04-20	Using the geno parser to get/parse the genotypes for the dataset	DannyArends

2016-04-20	Adding the geno file parser from Zach	DannyArends

2016-04-20	Creating the analysis object and passing results to the results template	DannyArends