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2017-11-22Added option to export csv of full mapping resultszsloan
2017-11-17Fixed issue that caused GEMMA LOCO to not work on productionzsloan
2017-11-06Replaced Histogram and Bar Chart with Plotly version and added new Box Plot ↵zsloan
with Plotly GEMMA now has option to select genotypes Updated dataset select dropdowns to be ordered correctly Fixed dataset select dropdowns for correlations to not show confidential datasets Added Skewness and Kurtosis to Basic Statistics table Fixed Verify and RNA-seq buttons on trait page Temporarily hardcoded Reference page until we get it to link with database
2017-09-22Fixed issue that caused covariates to not work for certain data set groupszsloan
2017-09-22Fixed issue that caused LOCO to not work when remapping or using single ↵zsloan
chromosome view
2017-09-21LOCO should work with GEMMA (when BIMBAM available), though I still need to ↵zsloan
do more testing
2017-09-14Committing current progress towards implementing LOCO for GEMMA, not done yetzsloan
2017-09-07Updated show trait page to correctly show GEMMA options for certain data setszsloan
2017-09-07Added the script to convert bimbam to kinship matriceszsloan
2017-09-05Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2017-09-05Added file converting genofiles to bimbamzsloan
2017-09-04gemma-wrapper: find binary in profilePjotr Prins
2017-08-29Mostly changes related to getting gemma working with covariates and BIMBAM ↵zsloan
file format Other changes include: - Fixing links in the network graph - Changing button colors on show trait page - Changing color scheme for heatmap - Making rows highlight in yellow when clicked on - Some changes to table appearance (like giving gene global search a horizontal scroll)
2017-07-06Merge branch 'testing' into developmentdevelopmentzsloan
2017-07-06Improved table appearance for global searcheszsloan
Scatterplot Matrix works again Added the first few changes to get covariates working (not done yet)
2017-06-30Fix Correlation Scatterplot axis formatLei Yan
2017-06-29Update Correlation ScatterplotLei Yan
2017-06-28Update Correlation ScatterplotLei Yan
2017-06-26Merge branch 'master' of github.com:genenetwork/genenetwork2Lei Yan
2017-06-26Fix Correlation Scatterplot thingsLei Yan
2017-06-14Changed color scale for heatmap to blue <-> white <-> redzsloan
Removed an extraneous character in the gsearch_pheno html
2017-06-14Removed scatterplot matrix option since it isn't working correctly right nowzsloan
Removed Download as PNG option for Probability Plot since it also isn't working yet
2017-06-14Added descriptions for GEMMA and PLINK as well as a warning about the issue ↵zsloan
with GEMMA where you can't run it simultaneously on two traits from the same group
2017-06-13Fixed trait links in network graph nodeszsloan
Added warning notifying users that file upload option in the submit_trait page doesn't work yet
2017-06-13Added to border to table footer in search resultszsloan
2017-06-13Fixed issue that caused haplotype analyst to no longer workzsloan
Fixed Results table for centimorgan results to display cM instead of Mb
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: 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
2017-05-21Merge 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
2017-05-08corr_scatter_plot update (use nvd3)Lei Yan
2017-05-04renamed: gn2_lei.conf -> gn2-lei.confLei Yan
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