| Age | Commit message (Expand) | Author |
|---|
| 2016-04-20 | Interval Mapping now correctly does interval mapping if Marker Regression isn......Changed "Manhattan Plot" label to "Marker Regr." to accurately reflect what the option does
| zsloan |
| 2016-04-20 | Added borders to stats table in trait page | zsloan |
| 2016-04-18 | Additive effect lines are now separated by chromosome (like the qtl line in t......Fixed order of stats table in trait page
Removed the qtl results table from chromosome view; will add the Interval Analyst output later
| zsloan |
| 2016-04-14 | Fixed issue where qtl lines in interval mapping wouldn't connect between chro......Added text explaining what * indicates in the mapping options menu
Removed ranges (log2 and fold) from stats table for phenotype traits
| zsloan |
| 2016-04-13 | Moved the code getting the description/location because it was throwing an er... | zsloan |
| 2016-04-13 | Global search should be able to return description and location columns now | zsloan |
| 2016-04-11 | Changed the way trait data is retrieved for the global search page (it now ge......This change increases the speed by a bit (85 seconds to 66 seconds for example)
Made the column width for location a bit wider for global search page so it doesn't spill onto a second line
| zsloan |
| 2016-04-07 | Added option to change the maximum y-axis value for GN1 mapping figure | zsloan |
| 2016-04-07 | Permutation figure and x-axis label should change to correctly reflect the ma......Fixed bug where broken image link would appear if you ran R/qtl with no permutations
| zsloan |
| 2016-04-07 | SNP Track option should now work for GN1 mapping figure...Fixed typo in show_trait html that caused the p-value slider to not work for correlations
| zsloan |
| 2016-04-06 | The option to switch between LRS and LOD for the GN1 mapping figure should no......The correct value (LRS or LOD) will now be displayed in the results table
Added glossary links for GN1 mapping figure options (permutations, bootstrap, etc)
| zsloan |
| 2016-04-06 | Setting lodm to always be 1.0 fixes the issue where it would incorrectly disp... | zsloan |
| 2016-04-06 | Permutations (suggestive/significant lines, legend, and histogram) should now......Changed the logic for receiving permutation/bootstrap info when loading mapping page in different ways (from show_trait, from remapping, from clicking single chromosome)
Added text below figure when Allele Effects selected/relevant
| zsloan |
| 2016-04-05 | Bootstrap test should now work correctly for qtl reaper mapping method on ful......There seems to be some issue with the way it does single chromosome bootstrap tests compared with GN1, though. It seems like GN1 completely re-runs the test for that specific chromosome, while GN2 just takes a subset from the previously calculated bootstraps
| zsloan |
| 2016-04-05 | Fixed issue where haplotype analyst option would appear when using genetic(ce... | zsloan |
| 2016-03-30 | Disabled Haplotype Analyst option if mapping scale is centimorgan/genetic | zsloan |
| 2016-03-30 | GN1 mapping now when mapping scale is centimorgan (for R/qtl)...Fixed some issues related to zooming in on chromosome X
Fixed problem where it threw an error for mapping methods that didn't return additive effect
Fixed problem where the endMb in the top form would be set to the endMb of the last chromosome when viewing full genome
| zsloan |
| 2016-03-29 | Additive effect option now works for GN1 mapping figure | zsloan |
| 2016-03-29 | Forgot to add GeneralObject file needed for haplotype analyst in last commit | zsloan |
| 2016-03-29 | Haplotype Analyst now works for GN1 mapping figure...Chromosome drop-down select and Mb range text fields now are set to the values the user last selected
| zsloan |
| 2016-03-28 | Legend option now works for GN1 mapping figure | zsloan |
| 2016-03-28 | Trait sample data table width now dynamically changes with number of attribut... | zsloan |
| 2016-03-24 | Graph width can now be set in Mapping Results | zsloan |
| 2016-03-24 | Add the Gene Track option to display the Gene Band for single chromosome view...Fixed an issue where width wasn't being set correctly, so chromosome view is correct width now (was too short before)
| zsloan |
| 2016-03-24 | Mapping results table is now limited to the top 200 markers; previously the p... | zsloan |
| 2016-03-23 | You can now select chromosome and an Mb range from the top menu and remap...The track in the single chromosome view to zoom into smaller intervals now works correctly again
| zsloan |
| 2016-03-23 | Fixed GN1 mapping plots so that Y axis and the Y coordinates of manhattan plo......Table filters markers so it can always be displayed now (previously was too large for GEMMA)
| zsloan |
| 2016-03-21 | Manhattan plot option now works for GN1 map, and GEMMA is set to display as m... | zsloan |
| 2016-03-21 | Changed code parsing marker csv file to increase GEMMA speed...Currently commenting out the vector map/table for GEMMA since they cause the page to hang, I'll try to figure out a way to prevent this
| zsloan |
| 2016-03-18 | Forgot to not retrieve sample data for the phenotype global search with the l... | zsloan |
| 2016-03-18 | Merge branch 'development' of github.com:genenetwork/genenetwork2 | zsloan |
| 2016-03-18 | Replaced header with other information in qtl map...Began adding menu to qtl map
Fixed global search to not retrieve samples (to increase speed)
Got the vector plot working again so it can be displayed alongside the gn1-style plot
Only display the vector plot when doing GEMMA to speed up (this might not be necessary)
| zsloan |
| 2016-03-17 | Fixed a bunch of geno files that had most of their contents removed for some ... | zsloan |
| 2016-03-15 | Merge branch 'development' of github.com:genenetwork/genenetwork2 | zsloan |
| 2016-03-15 | Merge branch 'master' of github.com:genenetwork/genenetwork2 | zsloan |
| 2016-03-15 | Merge branch 'master' of github.com:genenetwork/genenetwork2 into development | zsloan |
| 2016-03-15 | Merge branch 'master' of https://github.com/genenetwork/genenetwork2 | zsloan |
| 2016-03-15 | Fixed the mapping figure track that lets you zoom into a smaller range...Fixed the third party mapping figure tracks to refer to the correct chromosome (before it was always 1)
| zsloan |
| 2016-03-15 | Added mapping output file directory to gitignore | zsloan |
| 2016-03-14 | Changed the way headers look across all pages...Changed the way details are displayed in show trait page
Changed search query so that it orders results by symbol
| zsloan |
| 2016-03-03 | Fixed issue where correlation would do mapping if run after mapping | zsloan |
| 2016-03-03 | Merge branch 'master' of github.com:genenetwork/genenetwork2 into development | zsloan |
| 2016-03-03 | Fixed trait export to include SE values | zsloan |
| 2016-03-03 | Merge branch 'master' of https://github.com/genenetwork/genenetwork2 | zsloan |
| 2016-03-03 | Update gsearch.py | Lei Yan |
| 2016-03-02 | Increased gsearch speed by removing unnecessary query for sample data...Still slower than preferable due to having to query the gn1 database for every trait in the search results
| zsloan |
| 2016-03-01 | Merge branch 'master' of https://github.com/genenetwork/genenetwork2 | zsloan |
| 2016-03-01 | Committing change to dataset menu before pull | zsloan |
| 2016-03-01 | Fixed csv download and removed non-working "Download Table" button for collec......Not sure what the best way to determine the filename is, so just using "search_results" or "collection_list" for now
In future I want to replace the default csv download button by attaching its function to the previous "Download Table" button
| zsloan |
| 2016-02-26 | PLINK should not run correctly and graph using GN1 image...Updated dataset menu structure json
Increased the width for the label and text field for inputting MAF for PLINK and GEMMA
| zsloan |
