genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2015-07-02	Merge branch 'master' of github.com:genenetwork/genenetwork2	zsloan

2015-07-02	Merge pull request #81 from lomereiter/fix_exporting	zsloan
	Fix SVG/PDF exporting
2015-07-02	Combined searches that didn't work previously should work now, including cis ↵	zsloan
	and trans combined searches
2015-07-02	fix typos	Artem Tarasov

2015-07-02	fix #80	Artem Tarasov

2015-07-02	use button for returning to full view	Artem Tarasov

2015-07-02	added CairoSVG to misc/requirements	Artem Tarasov

2015-07-01	Needed to add a couple parenthesis for transLRS searches	zsloan

2015-07-01	Merge branch 'master' of github.com:genenetwork/genenetwork2	zsloan

2015-07-01	cis and trans LRS searches now work. Still need to get them working in ↵	zsloan
	combined searches
2015-06-29	Merge pull request #72 from lomereiter/issue69	zsloan
	Fixes #69
2015-06-29	Merge pull request #77 from lomereiter/fix_sql	zsloan
	SQL security fixes
2015-06-26	Fixed minor bug where the static loading bar would remain after the mapping ↵	zsloan
	results were displayed.
2015-06-26	Merge branch 'master' of github.com:genenetwork/genenetwork2	zsloan

2015-06-26	Fixed bug where mapping results sometimes wouldn't display. This would occur	zsloan
	due to a chromosome (in this case the last) not having any markers. Improved the way plink gets its path/command to use a method similar to the one Pjotr used with pylmm. I'll also do this for the other mapping methods. Fixed issue where the Y axis would always say LOD score. It now says LRS for mapping methods that return LRS Switched interval mapping (qtl reaper) to use the marker_regression template and removed the interval_mapping template (since it's unnecessary) Some commented out changes remain (in show_trait_mapping_tools and create_lodchart) from when I was attempting to open the mapping results in a new page. I had resolved every issue but the mapping javascript (lod_chart) not being able to access js_data (which has all the result data; markers, p-values, etc). I'm pretty sure that this is because js_data was inserted into the html after the page was loaded while the chart code ran immediately. I experimented with adding a short timeout to the mapping javascript and data table javascript, but while it worked for the table it did not work for the mapping figure. I don't know why this is.
2015-06-26	Added license file	pjotrp

2015-06-22	Merge branch 'master' of github.com:genenetwork/genenetwork2	zsloan
	Conflicts: wqflask/wqflask/templates/marker_regression.html
2015-06-22	Just a few minor changes before pulling Artem's fix to the mapping issue.	zsloan

2015-06-22	Merge pull request #75 from lomereiter/fix_search	zsloan
	fix genotype search
2015-06-22	Merge pull request #76 from lomereiter/fix_mapping_results	zsloan
	fix mapping results loading
2015-06-22	escape docs query	Artem Tarasov

2015-06-22	fixed a few potential security issues	Artem Tarasov

2015-06-21	fix mapping results loading	Artem Tarasov

2015-06-20	fix genotype search	Artem Tarasov

2015-06-18	Fixed issue that prevented multiple mapping submissions without refreshing. ↵	zsloan
	Also changed to where results open in new window instead of colorbox, though an issue remains where the css doesn't seem to be getting imported properly.
2015-06-18	removed unused function	Artem Tarasov

2015-06-18	fix all_samples_ordered	Artem Tarasov
	move duplicated code into a method, handle the case of missing f1/f12 correctly
2015-06-18	add missing line to webqtlUtil	Artem Tarasov

2015-06-17	Now you can expand/contract tabs on the trait page by click anywhere on the bar	zsloan

2015-06-16	Finished adding all the extra tools/links below the trait details	zsloan

2015-06-05	Added back in some of the options on the trait page; Add, Find, and Verify ↵	zsloan
	now work. I'll get the other 4 working next.
2015-06-04	Fixed a minor issue that was causing position search to not work.	zsloan

2015-06-02	Wildcards can now be appended to mRNA assay searches, but isn't working ↵	zsloan
	correctly yet with phenotypes
2015-06-02	Added Panduka's Genotation tool link to the trait page, along with the Gene, ↵	zsloan
	OMIM, and GenBank links
2015-06-02	Wildcard search should now work for Genotype searches	zsloan

2015-06-02	Wildcard search (*) works for regular mRNA assay and phenotype searches and ↵	zsloan
	fixed issue with black columns in correlation page
2015-05-26	Merge pull request #60 from lomereiter/pp	zsloan
	add missing file
2015-05-26	add missing file	Artem Tarasov

2015-05-26	Merge pull request #58 from lomereiter/pp	zsloan
	Use NVD3 for bar chart and probability plot
2015-05-26	fix terminology	Artem Tarasov

2015-05-26	use NVD3 for bar charts	Artem Tarasov
	added informative tooltips and error bars
2015-05-23	pp group selection	Artem Tarasov

2015-05-23	fix group selection in blocking by index	Artem Tarasov

2015-05-23	Fix trait grouping	Artem Tarasov

2015-05-23	new probability plot (using NVD3 library)	Artem Tarasov
	* z scores are computed on the client side (using jStat library) * added Shapiro-Wilk test results
2015-05-22	Fixed issue where correlation didn't work for human traits (and probably ↵	zsloan
	some others)
2015-05-21	Changed the digits for additive effect and megabases in the search results table	zsloan

2015-05-20	Merge pull request #53 from lomereiter/bar_chart_improvements	zsloan
	Bar chart improvements
2015-05-20	revert database.py setup	Artem Tarasov

2015-05-20	bar charts polished	Artem Tarasov
	* fixed bar chart width (two bars were invisible) * disabled basic stats update effects, if they are not visible * fix: unchecked samples were shown in charts (because attr('checked') was used instead of prop('checked')) * bar chart gets redrawn after checkbox changes * edit_data_change is also called when clicking buttons from the 'Block samples' panel * better bar chart transitions (use sample name as d3 key function)