genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2017-06-13	Fixed minor issue where the part of the legend describing the LRS/LOD line ↵	zsloan
	still appeared for manhattan plots
2017-06-12	Merge branch 'development' of github.com:genenetwork/genenetwork2 into ↵	zsloan
	development
2017-06-12	Added explanatory text to heatmap page	zsloan

2017-06-12	Fix binary paths for GEMMA_COMMAND, PYLMM_COMMAND and PLINK_COMMAND	Pjotr Prins

2017-06-12	Fixed issue where 0.0 values would be converted into X's on the trait page	zsloan

2017-06-09	Merge /home/staging/gene into development	zsloan

2017-06-09	- Changed the way the genofile is set so different genofiles can be selected ↵	zsloan
	for mapping - Now shows error page for Correlation Matrix if traits aren't all from the same group (later need to make it check for shared samples, since different groups may contain some of the same samples - Mapping results page now displays the genofile in the information section - Only show Interval Analyst if species is mouse or rat (previously it would show a blank table for other species) - Network Graph now only shows links in a node's info if the relevant information (for example geneid) exists, and the label changes depending on the type of data set - Other minor changes to the appearance of the Network Graph menu (less white space, plus clickable descriptions for a couple options) - Improved Correlations Results page to shorten Description and Authors cell content for Phenotype traits (to keep table width manageable) - Changed the glossary links for LRS and Additive Effect columns for Gene Global Search - Improved appearance for Phenotype Global Search results - Temporarily removed Mapping options/features that don't work from the trait page
2017-06-02	Merge branch 'master' of github.com:genenetwork/genenetwork2 into development	zsloan

2017-06-02	Merge branch 'master' of https://github.com/genenetwork/genenetwork2	zsloan

2017-06-02	settings: do not enforce JS paths	Pjotr Prins

2017-05-31	Merge branch 'master' of github.com:genenetwork/genenetwork2 into development	zsloan

2017-05-31	Added various tool options to correlation results page and improved table ↵	zsloan
	appearance for mRNA assay data sets (still need to improve it for others) Fixed minor logic issue in trait.py
2017-05-31	Merge branch 'master' of https://github.com/genenetwork/genenetwork2	zsloan

2017-05-31	JS_GUIX_PATH may not be there	Pjotr Prins

2017-05-31	Merge branch 'master' of https://github.com/genenetwork/genenetwork2	zsloan

2017-05-31	JS module handling	Pjotr Prins

2017-05-22	Merge branch 'master' of github.com:genenetwork/genenetwork2 into development	zsloan

2017-05-22	Added submit trait to header menu and fixed some minor issues with Network ↵	zsloan
	Graph interface
2017-05-22	Merge branch 'master' of https://github.com/genenetwork/genenetwork2	zsloan

2017-05-22	Added print lines showing url to views.py and updated dataset menu json file	zsloan

2017-05-21	Merge from the diet branch.	Pjotr Prins
	* refactored ./bin/genenetwork2 and /etc/default_settings - better detection of Guix - removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS - removing some default settings, such as PYLMM_COMMAND - rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY - added GUIX_JS_PATH for JS modules * Added documentation on installing binary GN2 * Updated Twitter board to latest version in Guix - it had broken * Updated many tools in the latest Guix profile
2017-05-16	Fixed issue that caused mapping to not work for R/qtl	zsloan
	Updated dataset menu dropdown info Began adding option to download statistics figures as PNG
2017-05-08	corr_scatter_plot update (use nvd3)	Lei Yan

2017-05-04	renamed: gn2_lei.conf -> gn2-lei.conf	Lei Yan

2017-05-04	Merge branch 'master' of github.com:genenetwork/genenetwork2	Lei Yan

2017-04-25	Fixed issue with correlation result trait links if target dataset is ↵	zsloan
	different from base dataset Improved collection list and view table appearances Added question mark image for glossary entries in table headers Fixed issue where extra decimal place sometimes appeared in bar chart Y axis tick values
2017-04-17	Added option to remove collections from collection list page	zsloan
	Improved appearance of search result and collection tables
2017-04-06	Merge branch 'master' of github.com:genenetwork/genenetwork2	Lei Yan

2017-04-05	Added images directory with various gifs, etc	zsloan

2017-04-05	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into development	zsloan

2017-04-05	- Temporary traits can be created, viewed, and added to collections	zsloan
	- Correct PCA trait data is created but can't be saved yet - Added inner margins by increasing xDomain and yDomain of probability plot on trait page - Increased X/Y-axis label font size - Turned "processes" to 0 on runserver.py for PROD setting, since it doesn't work with threading - Improved appearance of correlation page table - Added links to github to index page - Removed js_data from GEMMA/PLINK mapping results, since it isn't used for those - Removed "Tissue" from trait page for phenotype traits
2017-04-04	Change scatterplot title font size	Lei Yan

2017-04-04	Change scatterplot image buffer/inner	Lei Yan

2017-04-04	align X and Y meta info	Lei Yan

2017-03-30	Change "Correlation Scatterplot" size, font, color, etc.	Lei Yan

2017-03-16	Merge /home/zas1024/gene	Lei Yan

2017-03-16	Add meta info (X axis, Y axis) for Correlation Scatterplot	Lei Yan

2017-02-09	Fixed issue where I forgot to add GeneticType to the query_for_group query ↵	zsloan
	for non-mRNA Assay datasets Increased digits of some Basic Statistics values from 2 to 3
2017-02-09	Changed second column header to 'Value' when there's only one sample group	zsloan

2017-02-09	Added genetic_type to DatasetGroup object to differentiate between which ↵	zsloan
	groups should show dominance effect Minor changes/improvements for trait page Updated dataset_menu_structure.json
2017-02-08	Changed the way .fam files are written/read, which fixes the issue with ↵	zsloan
	GEMMA mapping accuracy.
2017-02-06	Mapping results figure now correctly says whether GEMMA was used as mapping ↵	zsloan
	method.
2017-02-06	Merge branch 'development' of github.com:zsloan/genenetwork2	zsloan

2017-02-06	Commented out reference to trait_submission since it's not used yet	zsloan

2017-02-06	Merge branch 'master' of github.com:zsloan/genenetwork2	zsloan

2017-02-06	Fixed appearance of several tables (search, mapping results, sample data)	zsloan
	Temporarily removed second sample table for CFW traits Fixed location of global search bar to work with wider screens
2017-02-02	Merge /home/zas1024/gene	Lei Yan

2017-01-26	Merge pull request #1 from genenetwork/testing	zsloan
	Various changes/fixes
2017-01-26	GEMMA now works with CFW data (had to update where it looks for the input ↵	zsloan
	files and how it writes the phenotype file) Y-axis for GEMMA now says -log(p) Updated the style of the trait sample data table in the trait page Updated dataset_select_menu_orig.js to also build just the Species and Group drop-downs for the trait input page (as opposed to all 4 drop-downs) Updated dataset menu json file Added option to show and hide columns to regular search page using colVis Changed regular and global search result table styles/column widths Began work on user trait submission code (not working yet though) Began work on static loading page for mapping results
2017-01-03	Fixed appearance of samples tables in show_trait to look like all the other ↵	zsloan
	tables Disabled sorting for the first column (check box) of the samples tables