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2017-06-13Fixed minor issue where the part of the legend describing the LRS/LOD line ↵zsloan
still appeared for manhattan plots
2017-06-12Merge branch 'development' of github.com:genenetwork/genenetwork2 into ↵zsloan
development
2017-06-12Added explanatory text to heatmap pagezsloan
2017-06-12Fix binary paths for GEMMA_COMMAND, PYLMM_COMMAND and PLINK_COMMANDPjotr Prins
2017-06-12Fixed issue where 0.0 values would be converted into X's on the trait pagezsloan
2017-06-09Merge /home/staging/gene into developmentzsloan
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
2017-06-02Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2017-06-02Merge branch 'master' of https://github.com/genenetwork/genenetwork2zsloan
2017-06-02settings: GENENETWORK_FILESPjotr Prins
2017-06-02settings: do not enforce JS pathsPjotr Prins
2017-05-31Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2017-05-31Added 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
2017-05-31Merge branch 'master' of https://github.com/genenetwork/genenetwork2zsloan
2017-05-31JS_GUIX_PATH may not be therePjotr Prins
2017-05-31Merge branch 'master' of https://github.com/genenetwork/genenetwork2zsloan
2017-05-31JS module handlingPjotr Prins
2017-05-22Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2017-05-22Added submit trait to header menu and fixed some minor issues with Network ↵zsloan
Graph interface
2017-05-22Merge branch 'master' of https://github.com/genenetwork/genenetwork2zsloan
2017-05-22Added print lines showing url to views.py and updated dataset menu json filezsloan
2017-05-22Merge pull request #254 from pjotrp/diet-mergezsloan
Merge from the diet branch
2017-05-21Merge 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
2017-05-16Fixed issue that caused mapping to not work for R/qtlzsloan
Updated dataset menu dropdown info Began adding option to download statistics figures as PNG
2017-05-08Merge pull request #253 from lyan6/masterzsloan
renamed: gn2_lei.conf -> gn2-lei.conf
2017-05-08corr_scatter_plot update (use nvd3)Lei Yan
2017-05-04renamed: gn2_lei.conf -> gn2-lei.confLei Yan
2017-05-04Merge branch 'master' of github.com:genenetwork/genenetwork2Lei Yan
2017-04-25Fixed 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
2017-04-17Added option to remove collections from collection list pagezsloan
Improved appearance of search result and collection tables
2017-04-06Merge branch 'master' of github.com:genenetwork/genenetwork2Lei Yan
2017-04-05Added images directory with various gifs, etczsloan
2017-04-05Merge branch 'testing' of github.com:genenetwork/genenetwork2 into developmentzsloan
2017-04-05Merge pull request #251 from lyan6/masterzsloan
Add meta info (X axis, Y axis) for Correlation Scatterplot
2017-04-05- Temporary traits can be created, viewed, and added to collectionszsloan
- 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
2017-04-04Change scatterplot title font sizeLei Yan
2017-04-04Change scatterplot image buffer/innerLei Yan
2017-04-04align X and Y meta infoLei Yan
2017-03-30Change "Correlation Scatterplot" size, font, color, etc.Lei Yan
2017-03-16Merge branch 'testing' of github.com:genenetwork/genenetwork2Lei Yan
2017-03-16Merge /home/zas1024/geneLei Yan
2017-03-16Add meta info (X axis, Y axis) for Correlation ScatterplotLei Yan
2017-02-09Merge pull request #247 from zsloan/masterzsloan
A couple minor commits
2017-02-09Fixed 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
2017-02-09Changed second column header to 'Value' when there's only one sample groupzsloan
2017-02-09Merge pull request #246 from zsloan/masterzsloan
Added genetic_type to DatasetGroup object to differentiate between wh…
2017-02-09Added 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
2017-02-08Merge pull request #245 from zsloan/masterzsloan
Changed the way .fam files are written/read, which fixes the issue wi…
2017-02-08Changed the way .fam files are written/read, which fixes the issue with ↵zsloan
GEMMA mapping accuracy.
2017-02-06Merge pull request #242 from zsloan/masterzsloan
Mapping results figure now correctly says whether GEMMA was used as m…
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