genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2015-06-22	fixed a few potential security issues	Artem Tarasov

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

2015-05-13	combine three similar queries into one	Artem Tarasov

2015-05-13	replace multiple tissue queries with a single one	Artem Tarasov

2015-05-13	cache datasets for each group	Artem Tarasov

2015-05-12	Resolved conflict before commit	zsloan

2015-05-12	Fix #35	Artem Tarasov
	* 'aliases' and 'location' are shown only where relevant * descriptions for phenotype datasets are provided at the top
2015-05-11	Moved chunks	Pjotr Prins

2015-05-11	Moving pylmm out of the tree	pjotrp

2015-04-10	Added git large file system (the .gitattributes files) and fixed an issue ↵	zsloan
	where rat trait pages wouldn't work
2015-03-27	Changed HTMLPATH in webqtlConfig since I forgot to in the last commit (since ↵	zsloan
	it used to point to the now-renamed 'web' directory). It obviously also needs to be renamed later, but I'll have to find every place that calls webqtlConfig.HTMLPATH first to do so.
2015-03-26	Removed several unused files from the base folder and their references in ↵	zsloan
	other files
2015-03-25	Pair scan image now loads properly	zsloan

2015-03-24	Change back port location and home directory location; this should be in ↵	zsloan
	external settings
2015-03-23	Updates to make GN2 work on my version of penguin (ports, and paths)	DannyArends

2015-03-17	Converting an absolute path to a relative path	DannyArends

2015-01-30	Fixed several bugs	Zachary Sloan
	Added legend to bar chart color by trait function Added scatterplot matrix figure Fixed database timeout problem
2014-12-12	Added a additive effect column to search result and collection tables	Zachary Sloan
	Fixed the header so that it looks fine when resizing
2014-11-17	Just more changes converting to bootstrap 3	Zachary Sloan

2014-10-17	Added reference, policies, and links pages	Zachary Sloan
	Improved the appearance of the header menu and "title bar"
2014-10-02	Fixed an error when there's no locus for mRNA expression traits	Zachary Sloan

2014-08-21	Committer: Lei Yan <lei@penguin.uthsc.edu>	Lei Yan
	On branch master
2014-08-21	Added the option to display mapping results as either an interval mapping	Zachary Sloan
	or manhattan plot Fixed a few minor bugs
2014-07-21	Fixed issue where sample values were ordered on the trait page	Zachary Sloan

2014-07-18	Merge /home/zas1024/gene	Lei Yan
	Conflicts: wqflask/base/data_set.py
2014-07-18	Added outlier highlighting	Zachary Sloan
	Changed order of tabs in statistics panel on trait page Started working on heatmap
2014-07-18	Correlation table for phenotypes is working	Lei Yan

2014-07-09	Updated coffeescript, svg export working fine, interval mapping zoom working	Zachary Sloan

2014-06-25	Added Karl's correlation matrix code	Zachary Sloan
	Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait
2014-06-06	Implimented Karl Broman's lodchart code for the interval mapping function.	Zachary Sloan
	Suggestive/significant bars and additive effect curve added
2014-05-05	Committing a bunch of changes related to integrating GEMMA and	Zachary Sloan
	adding the correlation matrix page
2014-02-28	Committing after creating AnonCollection class and before adding	Zachary Sloan
	remove trait function
2014-02-28	Made some changes/comments to Lei's load_genotypes.py file	Zachary Sloan

2014-02-27	Began working on a TraitCollection.py file that will contain both the	Zachary Sloan
	object for logged in user collections and collections created by anonymous users.
2014-01-30	Most of the work is done towards running lmm.py from the command line	Zachary Sloan
	and storing the results in redis
2014-01-29	Limited number of markers in marker regression result table to	Zachary Sloan
	those with a lod score > 2 Did some work towards adding the colored backgrounds to chromosome areas in the manhattan plot Changed the last two chromosomes for human manhattan plots to X and X/Y Started work on writing a script that can independently run the pyLMM code and store the results in redis
2014-01-23	Histogram is working	Zachary Sloan
	Fixed some bug with generating the manhattan plot for the HLC data set
2014-01-03	Wrote some code for the histogram figure	Zachary Sloan
	Changed some code in dataset to try and track down the issue with Amelie's file
2013-11-27	Clicking a trait in "color by trait" now gets all of its sample values	Zachary Sloan
	that will be used to color the bar graph
2013-11-26	Made some progress towards getting the traits inside a collection to display ↵	Zachary Sloan
	on hover
2013-11-25	Got the interval mapping results into a table	Zachary Sloan

2013-11-01	Merge /home/sam/gene	Zachary Sloan

2013-10-30	More work on collections	Sam

2013-10-25	Began working on color coding bar chart by extra attributes	Zachary Sloan

2013-10-15	Changed templates to call the header macro	Zachary Sloan
	Correlation page now works with Non-BXD (or whatever group) or All Samples options
2013-10-11	Merge /home/lei/gene	Zachary Sloan
	Conflicts: wqflask/maintenance/quick_search_table.py
2013-10-10	Almost have correlation working for non-primary strain/group	Lei Yan
	There's just some issue with parents/f1s not being included if you select non-BXD (or whatever the group is). All Samples, however does work.