genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2019-05-06	Added link to Affiliates section of index page	zsloan

2019-05-06	Made some changes Rob asked for to index page; reorganized some items and ↵	zsloan
	made news scrollable
2019-05-06	Removed some unused imports of htmlgen	zsloan
	Fixed a bug that sometimes occurred in search results Changed order of items on index page
2019-04-26	Issue where GEMMA LOCO mapping didn't work when samples were edited out ↵	zsloan
	should be fixed now
2019-04-26	Fixed issue where changed smaple values didn't show up in haplotype analyst ↵	zsloan
	results
2019-04-18	Fixed issue that caused removed strains to still appear in the haplotype ↵	zsloan
	analyst track
2019-04-12	Fixed PDF links in reference to point to the PDFs in GN1	zsloan

2019-04-12	- Improved Interval Analyst table appearance in mapping results	zsloan
	- Made the text on the "Forgot Password" page more simple and less cluttered - Added line to index page about RANGE search function - Fixed bar chart on trait page so that it sets the bottom margin depending upon the longest sample name length
2019-04-10	Removed option to upload file for submitting traits, since it doesn't ↵	zsloan
	currently work
2019-04-10	Fixed issue that was causing submitted temp traits to not work	zsloan

2019-04-05	Fixed issue that caused error for phenotype searches (kind of a quick fix ↵	zsloan
	and I do a try/except for whether it can build the trait object; ideally I should correctly filter out datasets)
2019-04-05	Fixed issue where Max LRS column displayed the mean in global search results	zsloan

2019-04-04	Fixed issue where dataset_menu_structure.json included some groups with no ↵	zsloan
	visible datasets
2019-04-03	Fixed an issue that caused global phenotype search to often not work and ↵	zsloan
	certain phenotype datasets to not show up in drop-downs
2019-04-03	Fixed issue where strains could be added twice in the SNP browser, causing ↵	zsloan
	some wonky behavior
2019-04-02	Fixed issue where non-GEMMA mapping would throw an error because it would ↵	zsloan
	still look for the results filename
2019-03-29	Fixed issue that caused PCA results to be different in GN2 than in GN1; one ↵	zsloan
	result needed to be transposed
2019-03-29	Updated UCSC Verify link-out from hg19 to hg38 for humans	zsloan

2019-03-28	Added link to GN2 document github wiki to index page	zsloan

2019-03-28	Possibly fixed issue where PCA traits didn't calculate for certain sets of ↵	zsloan
	traits
2019-03-27	Changed gen_select_dataset.py to be able to show multiple datasets under the ↵	zsloan
	Phenotype type (for example the GI Tract Metabolome data) Fixed issue where full description was given for some unpublished traits Fixed code related to editing certain pages (like news) with CKEditor, but it still won't work until the CKEditor library is included in GUIX or something
2019-03-25	- Added SVG export to basic stats figures	zsloan
	- Fixed issues where some stats figures (mainly box and violin plots) didn't update correctly when sample values were changes - Fixed issue with some temp traits if user wasn't logged in - Fixed issue where traits couldn't be added to a collection from the correlation results page
2019-03-19	Added option to add PCA traits to collection from correlation matrix page	zsloan

2019-03-18	- Added PCA traits to correlation matrix. You can't change their names yet ↵	zsloan
	or add them to a collection from the corr matrix page, but you can click them and access them from the trait page. I'll add the option to access them from the corr matrix page as well, but adding the option to change their names might be trickier since they're currently used as their Redis keys. I need some better way of passing the Redis key around so it can be stored in collections, but this is tricky without changing the structure in ElasticSearch - Fixed the way temp traits work so you can use them with various functions, like mapping, correlations, network graph, etc - Fixed some appearance issue where the network graph options were too wide if a trait name was too long
2019-03-13	Zooming into chromosome or remapping with GEMMA is now very fast, since it ↵	zsloan
	stores the output file Added option to search for terms in quotes, searching for all the contents within the quotes Added link to R/qtl documentation when user is in the R/qtl mapping tab
2019-03-11	Changed header style, because the jumbotrons previously used didn't look ↵	zsloan
	that good. Now it's just a simple header element.
2019-03-11	Added default empty collection when user is logged in and attempts to add ↵	zsloan
	traits to a collection Fixed issue with displaying cofactor selection tables for scatterplot Removed limit on text length for collection trait fields (dataset name and description)
2019-03-07	Changed the way covariates are displayed when selected for mapping	zsloan
	Made the outlier notification appear for all mapping methods Removed some misleading text saying "Block samples" from the Transform and Filter Data section
2019-03-07	Made violin plots for different groups/sample-sets different colors and ↵	zsloan
	matched colors between box and violin plots
2019-03-07	Fixed issue where pressing enter in the search page text area would go to a ↵	zsloan
	new line before submitting Also removed some pointless wrapper from dataset_select_menu_orig.js that was left over from being converted from coffeescript (need to do this with other files also)
2019-03-07	Fixed issue where correlation results containing NaN results sorted incorrectly	zsloan
	Set default permutations for R/qtl to 200
2019-03-06	Cofactor option for correlation scatterplot was broken; it should be fixed now	zsloan
	Added title to basic stats table and made link for Interquartile Range more obvious Removed pointless "Delete Collection" button from correlation results page
2019-03-05	Made R/qtl metho/model names better and added some javascript to disable ↵	zsloan
	wrong combinations of options
2019-03-04	Fixed excel export to show all columns	zsloan
	Fixed stats table to calculate Range and Interquartile Range correctly, and only show Range (fold) for appropriate traits
2019-03-04	- Added z-score transformation	zsloan
	- Added text indicating which transformation has been applied
2019-03-01	Added alternating point colors for manhattan plots	zsloan

2019-03-01	Changed loading page to work for any feature, instead of having to make a ↵	zsloan
	separate one like I did for correlation previously Fixed some wrong text on heatmap page
2019-03-01	Added more information to the top-right corner of the mapping results	zsloan
	Fixed sorting issues on correlation page
2019-02-27	Added loading page for correlation	zsloan
	Added a better error page for mapping if no results are returned (which generally implied an error occurred during the running of GEMMA) Fixed some issues with tables, like them sorting incorrectly or showing the wrong number of digits
2019-02-22	Fixed some appearance issues with several tables	zsloan
	Fixed issue where cofactor selection screens were broken Changed case attributes to be applied across groups, though need to discuss this with Rob since it shouldn't always be done this way Added new inversion transformation
2019-02-18	Updated installation instructions and SERVER_PORT for single flask server	Pjotr Prins

2019-02-15	Fixed error caused by change to N values in database (now takes strings ↵	zsloan
	instead of integers) Fixed error that caused N to show up as "null" in the trait sample table instead of "x"
2019-02-14	Fixed minor bug with updating stats figures when sample values changed	zsloan

2019-02-14	Changed trait page tables to load JSON	zsloan
	Also fixed such that sorting works with user-updated values
2019-02-13	Removed pylmm references and related functions	Pjotr Prins

2019-02-13	Remove all coffee files	Pjotr Prins

2019-02-12	Added GeneWeaver linkout	zsloan
	Fixed some issues with sorting in various tables Changed header appearance for some pages Fixed bug where basic stats table would sometimes be duplicated or show up with empty fields
2019-02-05	Removed redundant header text from search page to save vertical space	zsloan

2019-02-05	Fixed issue with getting marker info that affected heatmap and possibly ↵	zsloan
	other functions Added the collection page features (correlation matrix, network graph, third party link-outs, etc) to the search result and correlation result pages
2019-02-04	Changed the way the table is drawn for the search pages so that it can show ↵	zsloan
	when loading and more easily control cell contents Added typeahead to snp_browser (still need to tell it only to use it for rat, though) Added WebGestalt link to collection page (still need to add it and BNW to other trait list pages)