genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2016-03-03	Merge branch 'master' of https://github.com/genenetwork/genenetwork2	zsloan

2016-03-02	Increased gsearch speed by removing unnecessary query for sample data	zsloan
	Still slower than preferable due to having to query the gn1 database for every trait in the search results
2016-02-25	fixed untracked files	zsloan

2016-02-04	Most importantly, this commit fixes an issue that caused the trait page to ↵	zsloan
	not work because of the new dataset_menu_structure.json file An Intro section is also added to the header, though for the time being its contents aren't populated and the edit option isn't working
2015-12-14	GN1 mapping full genome figure now correct for pylmm and output to web page	zsloan

2015-12-12	Changed loop drawing qtl curve to fix some issues; still need to make it ↵	zsloan
	draw to different chr areas though
2015-11-18	Fixed issue where literature and tissue correlation didn't work	zsloan
	Scatterplot matrix feature only appears if user is logged in now Committing current progress on mapping page (it can at least import the file now, but there are still errors)
2015-11-09	Fixed issue that caused mapping to not work; for some reason the path to ↵	zsloan
	pylmm was wrong
2015-10-12	Changed the location filter for correlation page	zsloan

2015-09-11	Comment out some excessive stdout spam	DannyArends

2015-09-10	Fixed "TypeError: float argument required, not NoneType" about mean.	Lei Yan
	Committer: Lei Yan <lei@penguin.uthsc.edu> On branch master
2015-08-26	Fixed issue with colums for the gene global search (still need to change for ↵	zsloan
	phenotype) Fixed issue where LRS and LOD are sometimes labeled incorrectly Changed the header of the trait page Added link to GN1 in header Fixxed an issue that made permutations not work with pylmm Fixed "sign in" button when creating a collection while not logged in
2015-07-20	Fixed the code that generates the dataset selection drop-down for correlations	zsloan
	Made changes to the tables of correlation results, collections, and search results: - Added resizeable columns to correlation results and collections, but not to search results because it seems that it requires Y scrolling to be set (I'll check if it makes sense to add scrolling to the search results) - Correlation results and collections are now in scrolling tables - The style is the same across all of these tables now Remaining issues: - It doesn't seem like I can set the column width when initializing dataTables in correlation results. I don't know why this is; it might be due to the table already being the size of a full page. I want to be able to default to some good widths, even if the user can resize them - I tried adding hoverForMore, but it doesn't seem to cooperate with datatable cells; I think this is due to having to put the text in a div.
2015-07-10	Fixed the genofile_parser.py script since some .geno files had been ↵	zsloan
	incorrectly converted to json Fixed GO search to work with combined searches
2015-07-09	Mapping methods now check for existing genotype files.	zsloan
	Currently we still usually get our samplelists from the genofile. This is dumb because it results in us having a bunch of "dummy" genofiles for certain data sets (seems to be mostly human ones). This means that checking for the genofile alone isn't enough to determine if a mapping method should exist for a given group I wrote some code that will instead get the samplelist from the plink .fam file for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy .geno files, but we can't yet do so because it's currently the only place we seem to be storing the sample list for some groups. I also moved gemma into the plink directory to get it out of the git tree. Since it uses the same files as plink, it doesn't make sense for it to be in its own separate directory
2015-07-09	Some phenotype searches were throwing an error due to an assert statement in ↵	zsloan
	trait.py. Since I couldn't find the purpose of the assert statement I removed it.
2015-07-07	Added index column and changed the way location is displayed for search results	zsloan

2015-06-29	Merge pull request #72 from lomereiter/issue69	zsloan
	Fixes #69
2015-06-22	fixed a few potential security issues	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
2015-05-26	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