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2015-10-08Committer: Lei Yan <lei@penguin.uthsc.edu>Lei Yan
On branch master
2015-10-08Using the correct NA from Rpy2DannyArends
2015-10-08Minor, adding a better check for NADannyArends
2015-10-08Adding more commentsDannyArends
2015-10-08Merge branch 'master' of github.com:genenetwork/genenetwork2 into ↵DannyArends
WGCNAintegration
2015-10-08User inputs are now passed to the algorithm, and power is tested, and ↵DannyArends
autoselected. We need to discuss which parameters we want to expose to the user.
2015-10-08Massive update to the templates, adding error checking and handling + the ↵DannyArends
eigen genes per module
2015-10-07Adding library for slider used with correlation toolzsloan
2015-10-07The results now show the soft thresholds table, and the gene <-> module tableDannyArends
2015-10-07Passing more information calculated by WGCNA to the results pageDannyArends
2015-10-07Merge branch 'master' of github.com:genenetwork/genenetwork2 into ↵DannyArends
WGCNAintegration
2015-10-05Correlation Matrix page is partially complete + fixed some issues with ↵zsloan
column resizing on global search pages
2015-09-27Merge branch 'master' of github.com:genenetwork/genenetwork2 into ↵DannyArends
WGCNAintegration
2015-09-25Forgot to add the table-striped class to the basic stats table to make its ↵zsloan
style the same as other tables
2015-09-25Made the basic statistics table look nicer and got rid of the foo column if ↵zsloan
only one sample group
2015-09-24Location range feature should work for correlations now, though the ↵zsloan
interface appearance needs to be improved
2015-09-20Using the webqtlConfig.TMPDIR constant and the webqtlUtil.genRandStr functionDannyArends
2015-09-20Now able to run WGCNA analysis on a user defined collection, still lots of todosDannyArends
2015-09-20Display the results from WGCNA updatedDannyArends
2015-09-20Transfering data from python to R for WGCNA analysis using Rpy2DannyArends
2015-09-20Updating the WGCNA setup and results templatesDannyArends
2015-09-19Adding a todo list to the code, for issue: genenetwork/genenetwork2#119DannyArends
2015-09-19Adding views and passing the trait_list information from setup to resultsDannyArends
2015-09-192 templates, 1 for user input and 1 for showing the resultsDannyArends
2015-09-19Merge branch 'master' of github.com:genenetwork/genenetwork2 into ↵DannyArends
WGCNAintegration
2015-09-18Filter by min expression and r range now works, though interface for slider ↵zsloan
could be improved
2015-09-17Merge branch 'master' of github.com:genenetwork/genenetwork2 into ↵DannyArends
WGCNAintegration Staying up2date
2015-09-11Merge branch 'master' of github.com:genenetwork/genenetwork2zsloan
2015-09-11Fixed issue causing error if trying to use Heatmap or Correlation Matrix ↵zsloan
with an empty collection Fixed tables in correlation page and trait page to separate index column and checkbox column
2015-09-11Removing import pandas from codeDannyArends
2015-09-11More fiddling with templatesDannyArends
2015-09-11Figured out how those flask templates work, analysis broken down into 3 ↵DannyArends
parts, WGCNA R package installs and loads succesfully in the gn2-docker image
2015-09-11Some more work on the analysisDannyArends
2015-09-11Start R and load the WGCNA library in wgcna_analysis.pyDannyArends
2015-09-11Adding empty WGCNA class, and creating it in views.pyDannyArends
2015-09-11Seems I always turn around the G and CDannyArends
2015-09-11Adding a custom wgcna route in gn2, and adding a button to the ↵DannyArends
collections/view.html
2015-09-11Comment out some excessive stdout spamDannyArends
2015-09-11Adding an empty HTML results template for WCGNADannyArends
2015-09-10Merge pull request #117 from lyan6/masterzsloan
Fixed "TypeError: float argument required, not NoneType" about mean.
2015-09-10Fixed "TypeError: float argument required, not NoneType" about mean.Lei Yan
Committer: Lei Yan <lei@penguin.uthsc.edu> On branch master
2015-09-09Issue genenetwork/genenetwork2#113, forgot to uncomment the secret_keyDannyArends
2015-09-09Fix for issue genenetwork/genenetwork2#113, I added the SESSION_TYPE and ↵DannyArends
SECRET_KEY to the default config, this should be overwritten in my_settings.py
2015-09-08Fixed covariates with R/qtl mappingzsloan
A few minor GUI changes on trait page (button names, locations, etc) Fixed "pressing enter to search" on index page
2015-09-01Fixed issue that caused R/qtl mapping to not workzsloan
Removed bootstrap and additive effect options until I can get them working correctly
2015-09-01Fixed color by trait featurezsloan
Added Y axis line to bar histogram Added link to GN1 in menu bar Fixed mapping results table to look more like other tables (though still has initial issue with header being too short) Added Tissue to global search results and trait page
2015-08-26Fixed issue with colums for the gene global search (still need to change for ↵zsloan
phenotype) Fixed issue where LRS and LOD are sometimes labeled incorrectly Changed the header of the trait page Added link to GN1 in header Fixxed an issue that made permutations not work with pylmm Fixed "sign in" button when creating a collection while not logged in
2015-08-14Added csv download button to search result table; still need to add to otherzsloan
tables and later attach its functionality to the existing Download Table button Fixed an issue where rows wouldn't uncheck with backspacing in Select Top text area; the last commit just fixed the highlighting, not the checkboxes Some changes in progress towards trying to fix the additive effect issue; the problem is that the lod_chart.js code writes each chromosome as one d3 path, so I can't change the color for individual segments within that path. I'll have to completely change the way the path is drawn for the additive effect
2015-08-12Made Select Top function more intuitively and changed the text box lengthzsloan
2015-08-12Fixed global and regular search so that resizing/reordering columns works ↵zsloan
for all of them, among other minor changes
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