| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2016-04-06 | Permutations (suggestive/significant lines, legend, and histogram) should ↵ | zsloan | |
| now work for both R/qtl and qtl reaper mapping. 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 | |||
| 2016-04-05 | Bootstrap test should now work correctly for qtl reaper mapping method on ↵ | zsloan | |
| full genome view 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 | |||
| 2016-04-05 | Fixed issue where haplotype analyst option would appear when using ↵ | zsloan | |
| genetic(centimorgan) mapping | |||
| 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) | zsloan | |
| 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 | |||
| 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 | zsloan | |
| Chromosome drop-down select and Mb range text fields now are set to the values the user last selected | |||
| 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 ↵ | zsloan | |
| attributes and standard error | |||
| 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 | zsloan | |
| Fixed an issue where width wasn't being set correctly, so chromosome view is correct width now (was too short before) | |||
| 2016-03-24 | Mapping results table is now limited to the top 200 markers; previously the ↵ | zsloan | |
| page took a long time to load when there were too many markers | |||
| 2016-03-23 | You can now select chromosome and an Mb range from the top menu and remap | zsloan | |
| The track in the single chromosome view to zoom into smaller intervals now works correctly again | |||
| 2016-03-23 | Fixed GN1 mapping plots so that Y axis and the Y coordinates of manhattan ↵ | zsloan | |
| plot points are correct Table filters markers so it can always be displayed now (previously was too large for GEMMA) | |||
| 2016-03-21 | Manhattan plot option now works for GN1 map, and GEMMA is set to display as ↵ | zsloan | |
| manhattan plot | |||
| 2016-03-21 | Changed code parsing marker csv file to increase GEMMA speed | zsloan | |
| 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 | |||
| 2016-03-18 | Forgot to not retrieve sample data for the phenotype global search with the ↵ | zsloan | |
| last commit, added it now | |||
| 2016-03-18 | Replaced header with other information in qtl map | zsloan | |
| 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) | |||
| 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 | zsloan | |
| Fixed the third party mapping figure tracks to refer to the correct chromosome (before it was always 1) | |||
| 2016-03-14 | Changed the way headers look across all pages | zsloan | |
| Changed the way details are displayed in show trait page Changed search query so that it orders results by symbol | |||
| 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 | zsloan | |
| Still slower than preferable due to having to query the gn1 database for every trait in the search results | |||
| 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 ↵ | zsloan | |
| collections list, collection view, gene/pheno global search, and regular search 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 | |||
| 2016-02-26 | PLINK should not run correctly and graph using GN1 image | zsloan | |
| Updated dataset menu structure json Increased the width for the label and text field for inputting MAF for PLINK and GEMMA | |||
| 2016-02-25 | fixed untracked files | zsloan | |
| 2016-02-24 | GEMMA mostly working with gn1 mapping, though there may be some issue with ↵ | zsloan | |
| the y scale | |||
| 2016-02-18 | Edited gen_select_dataset to remove confidential datasets | zsloan | |
| Also hard-coded the removal of Macaque Monkey since I couldn't think of a good way to retroactively check if every dataset in a species is confidential | |||
| 2016-02-15 | Fixed R/qtl mapping so the group (BXD, etc) isn't hardcoded | zsloan | |
| Removed an extraneous </td> tag from the show trait page | |||
| 2016-02-11 | Updated jquery validation plugin, now works in IE | zsloan | |
| Fixed a couple minor html syntax erors in login_user.html and base.html Changed export button on correlation page to csvHtml5, but still has problem with commas in fields being interpreted as a new column | |||
| 2016-02-08 | Fixed the logic if how the correlation page applies filters (mean ↵ | zsloan | |
| expression, location, etc) Added back some colorbox directories that we apparently need (I had removed them in an earlier commit) | |||
| 2016-02-08 | Merge branch 'master' of github.com:genenetwork/genenetwork2 into development | zsloan | |
| Conflicts: .gitignore | |||
| 2016-02-08 | gitignore: resolved conflict | pjotrp | |
| 2016-02-04 | Most importantly, this commit fixes an issue that caused the trait page to ↵ | zsloan | |
| not work because of the new dataset_menu_structure.json file An Intro section is also added to the header, though for the time being its contents aren't populated and the edit option isn't working | |||
| 2016-01-29 | Info button should now work for phenotype and genotype datasets | zsloan | |
| 2016-01-27 | Merge branch 'master' of github.com:genenetwork/genenetwork2 into development | zsloan | |
| 2016-01-27 | Added info button to Dataset dropdown on index page | zsloan | |
| Fixed script that generates dataset dropdown json file to include accession id Fixed dataset link on search results page | |||
| 2016-01-26 | Removed a bunch of files/directories/packages that are no longer used and ↵ | zsloan | |
| some corresponding imports | |||
| 2016-01-19 | Adding Python setup.py support | pjotrp | |
| 2016-01-15 | Cofactor now works with reaper | zsloan | |
| 2016-01-14 | Regular and single chr views work for qtl reaper now | zsloan | |
| Single chr now works for R/qtl (didn't before) Merged qtl reaper code into marker_regression.py | |||
| 2016-01-12 | Mapping works for rqtl and centimorgan scale | zsloan | |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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