genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2016-11-08	Adding the joss badge	DannyArends

2016-11-07	Adding functions addNode and addEdge, to separate out the cytoscape graph ↵	DannyArends
	creation from the main CTL analysis code
2016-11-07	Adding the reference to the paper, and updating the output to show the ↵	DannyArends
	cytoscape.js network
2016-11-07	Adding code to the ctl analysis file to output nodes and edges for cytoscape	DannyArends

2016-11-07	Javascript file (based on the correlation file) to dsplay CTL networks using ↵	DannyArends
	cytoscape.js
2016-10-31	Merge branch 'lyan' into testing	Pjotr Prins

2016-10-31	Use existing GENODIR - the metadata can be stored there, next to the	Pjotr Prins
	.geno files.
2016-10-31	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing	Pjotr Prins

2016-10-31	Fix spacing	Pjotr Prins

2016-10-31	Merge branch 'master' of github.com:lyan6/genenetwork2 into lyan	Pjotr Prins

2016-10-29	For those case that we have multiple genotypes we would like to add a selector.	Lei Yan

2016-10-25	Just removed some extraneous spaces in trait.py	zsloan

2016-10-25	Replaced the Download Table button for collection page with python version ↵	zsloan
	that displays metadata, etc Removed currently unused javascript and css imports related to the DataTables buttons import (since it was replaced with the python export) from regular search, both global searches, and the view_collection page Added a bunch of parameters to the jsonable function for the GeneralTrait object in order to later create a json version of the search results and implement the client-side Scroller feature (which dynamically loads table rows from json when you scroll)
2016-10-21	Added CSV table download option to both gene and pheno global search	zsloan
	The "Database" part of the metadata isn't displayed for global search table downloads In both regular and global search, the table can not be sorted by whether the first column is checked Removed some unused datatables/javascript from the regular and global search page html
2016-10-21	Added metadata to "Download Table"	zsloan
	Only checked traits are now downloaded and all traits are downloaded if nothing is checked
2016-10-19	Rewrote export CSV in python	zsloan
	Still need to add metadata and change it to where only selected traits are exported
2016-10-17	Fixed issue where period sometimes appeared incorrectly in search results text.	zsloan
	Changed formatting of a couple things in search results text (capitalizing/underlining "terms" and bolding the search term) Changed "Gene" label on trait page to "NCBI" and removed GenBank link
2016-10-15	Remove all spacing introduced by merge	Pjotr Prins

2016-10-13	Merge branch 'master' of github.com:zsloan/genenetwork2 into zsloan	Pjotr Prins

2016-10-12	Moved plink code out of marker_regression, though I don't think plink is ↵	zsloan
	working right now Ran some end of line conversion on rqtl_mapping because there were a few ^M's
2016-10-12	Removed unused gemma code from marker_regression.py and changed the order of ↵	zsloan
	a couple functions in collect.py to more accurately reflect when they're called
2016-10-11	Merge branch 'pjotr-gn2' into testing	Pjotr Prins

2016-10-09	Handle VERSION on different pages	Pjotr Prins

2016-10-09	Merge branch 'mechanize' into testing	Pjotr Prins

2016-10-09	Revert on Zach tabs and trailing spaces	Pjotr Prins

2016-10-09	CTL: show correct # of phenotypes also in results page	Pjotr Prins

2016-10-09	Add version information	Pjotr Prins

2016-10-09	Merge branch 'master' of github.com:zsloan/genenetwork2 into zsloan	Pjotr Prins

2016-10-09	Changed mirrors & affiliates on wqflask/wqflask/templates/index_page_orig.html	Pjotr Prins

2016-10-09	Merge branch 'twitter' into pjotr-gn2	Pjotr Prins

2016-10-09	Merge branch 'testing' into twitter	Pjotr Prins

2016-10-09	Changed mirrors & affiliates on wqflask/wqflask/templates/index_page_orig.html	Pjotr Prins

2016-10-09	Added links to base.html	Pjotr Prins

2016-10-07	Removed qtlreaper code from marker_regression and moved it to a separate file.	zsloan
	Fixed CTL template to display correct number of traits (previously it would display 1 fewer than you selected).
2016-10-07	Make sure JS path exists	Pjotr Prins

2016-10-07	Twitter: added news list to search page	Pjotr Prins

2016-10-07	Tweets on main page are working	Pjotr Prins

2016-10-07	Changed error output	Pjotr Prins

2016-10-07	Saner handling of TMPDIR and TEMPDIR	Pjotr Prins
	Throw error when TMPDIRs are not writable
2016-10-06	URLs: replaced non-functioning URLs	Pjotr Prins

2016-10-06	Footer: updating URLs	Pjotr Prins

2016-10-06	Do not open new page in browser on URL	Pjotr Prins

2016-10-06	Removed dead URL	Pjotr Prins

2016-10-06	URL: replaced dead Memphis URL with current GN2 machine	Pjotr Prins

2016-10-06	URL: prevent opening new pages	Pjotr Prins

2016-10-06	URL: updated Amigo reference on front page	Pjotr Prins

2016-10-06	URLs: update GO database URL and removed opening new browser pages	Pjotr Prins

2016-10-06	Logger: add more granular debug messages	Pjotr Prins

2016-10-06	CTL requires 2 traits minimally. Also use traits/phenotypes consistently	Pjotr Prins

2016-10-05	CTL now displays proper error if fewer than 4 traits are selected. Also, ↵	zsloan
	WGCNA previously incorrectly gave an error when fewer than 5 traits were selected instead of fewer than 4 (because it said '<= 4'). I also improved the formatting for the html for both CTl and WGCNA Analysis.