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2016-06-15Menu: populating tissue from RESTPjotr Prins
2016-06-15Menu: refactoring code, handling errorPjotr Prins
2016-06-14Added y axis line to probability plot and bar chartzsloan
Automatically determines number of decimal places to show on y axis of probability plot; still need to figure out how to do it with bar chart Added some logging to figure out MySQL connection issue
2016-06-14Menu: fetch group info from serverPjotr Prins
2016-06-14Make species section in data structurePjotr Prins
2016-06-14Menu: fetch species from gn_serverPjotr Prins
2016-06-07R/qtl pair scan now works again, though it takes a while (10-15 minutes).zsloan
Added pop-up warning user about run-time for pair scan Fixed links to GN2 github on the index page Fixed a couple issues with the search result page text Changed the appearance of the trait sample data table to match other tables (darker headers, etc)
2016-06-03Made a bunch of changes to correlation and search result tables (mainly the ↵zsloan
former) and made all tables a little more compact by lessenning the padding
2016-06-03Changed appearance of tables to more easily differentiate them from the rest ↵zsloan
of the page (still not totally pleased with them though) Fixed issue where some N/A lrs scores and additive effects were being changed to 0's, which was misleading and kept them from always being sorted at the bottom. They now appear as N/A.
2016-06-02Fixed some issues with global search result tables, including:zsloan
- Wrong digits for mean expression and additive effect - Bad loooking width on some columns, like Max LRS Location - Janky functionality for column resizing and drag-and-dropping (just disabled these functions) - Geno and Pheno global search tables weren't built in the same way, so now they are I also fixed the sorting to always put N/A's at the bottom of the table by editing naturalSort.js
2016-06-01Changed global gene search to no longer use server-side processingzsloan
2016-05-31Fixed error when MrnaAssay search results didn't have a geneidzsloan
2016-05-31Renamed TEXTDIR to GENERATED_TEXT_DIRPjotr Prins
2016-05-31Allow the json dir to be in the old location.Pjotr Prins
2016-05-27Fixed issue where the Non-BXD (or whatever group/inbred set) table would ↵zsloan
show up when there should be no such samples Fixed Interquartile Range link in basic statistics table
2016-05-27Improved appearance of p values below slider in correlation menu on trait ↵zsloan
page. The way I did it is really awful (a bunch of  's) but nothing else seemed to work, including putting a div or span with a fixed width between them
2016-05-26Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-05-26Merge branch 'master' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-05-26Merge branch 'master' of https://github.com/genenetwork/genenetwork2zsloan
2016-05-26Issue with certain samples (like BXD65a, ones were there are multiple for a ↵zsloan
single BXD or whatever) should be fixed for different mapping methods and data set types Renamed directories with genotypes so tools.py didn't need to be changed (which might mess up other deployments) Fixed error when searching genotype data sets
2016-05-23Reaper mapping results are now correct and account for samples with two ↵zsloan
names (like BXD65a) R/qtl and PYLMM still not working with the change and bootstrap results are also still wrong, so need to fix those issues.
2016-05-18Merge branch 'staging' of https://github.com/genenetwork/genenetwork2zsloan
2016-05-18Updated dataset selection dropdown menus and fixed error caused by traits ↵zsloan
with no description
2016-05-17Merge branch 'staging' of github.com:genenetwork/genenetwork2 into developmentzsloan
2016-05-17Merge branch 'staging' of github.com:genenetwork/genenetwork2zsloan
2016-05-17Correlations are now much faster after I disabled fetching the sample data ↵zsloan
for each result trait
2016-05-13Fixed path for IM bar plotPjotr Prins
2016-05-13Removing ref. to HTMLPATHPjotr Prins
2016-05-13WebqtlConfig.py: Constant handlingPjotr Prins
2016-05-13Fix paths for imagesPjotr Prins
2016-05-10Correlation successfully uses materialized views and parallel processing, ↵zsloan
but for some reason is taking an immense amount of time so need to troubleshoot that Changed order of mapping options to display Interval Mapping first Changed some links to no longer open in new tab/window
2016-05-10Merge branch 'master' of github.com:genenetwork/genenetwork2 into merge_zachPjotr Prins
2016-04-29Fixed database link in trait page detailszsloan
2016-04-29Also fixed links in statistics section (for normal probability plot) and ↵zsloan
removed 'target=_blank's
2016-04-29Fixed links in correlation descriptions on trait page and removed ↵zsloan
target=_blank (so will not open in new window unless user specifies) Fixed javascript so description changes when user changes the method and "Type" option is removed for literature correlation
2016-04-29URL: removed _blank from first URLPjotr Prins
2016-04-29Updated mailing list URLPjotr Prins
2016-04-29Plotting: using cairo-png for headless environmentsPjotr Prins
2016-04-29MergePjotr Prins
2016-04-28Added option to export permutation results for mapping pagezsloan
Added data_scale to dataset objects and basic stats table will now check data scale when calculating range Made interval analyst results table work with datatables Changed the appearance of the basic stats table some by giving it a border
2016-04-28Changed the defunct GeneRIF URL to a working Wikipedia URL (whichPjotr Prins
also points to the non-working NCBI link)
2016-04-26Interval mapping: fix font and image pathPjotr Prins
2016-04-26Merging with Zach's latest branchPjotr Prins
2016-04-25Interval Analyst table mostly working, just need to work out a few more thingszsloan
2016-04-22Fixed issue where manhattan plot setting wasn't being carried over to single ↵zsloan
chromosome view for mapping results Removed a useless "if 1 == 1" line that was in marker_regression_gn1.py for testing.
2016-04-20Interval Mapping now correctly does interval mapping if Marker Regression ↵zsloan
isn't checked (it used to just "connect the dots" of the marker regression output) Changed "Manhattan Plot" label to "Marker Regr." to accurately reflect what the option does
2016-04-20Added borders to stats table in trait pagezsloan
2016-04-20Fix typoPjotr Prins
2016-04-20A few fixes to get the webserver running againPjotr Prins
2016-04-20Add filePjotr Prins
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