| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2016-04-20 | [PATCH 026/100] Introducing cached values PYLMM_COMMAND, | Pjotr Prins | |
| GEMMA_COMMAND, PLINK_COMMAND and TEMPDIR | |||
| 2016-04-20 | Introducing TEMPDIR | pjotrp | |
| 2016-04-20 | [PATCH 024/100] Sanitizing file handling | Pjotr Prins | |
| 2016-04-20 | [PATCH 023/100] WIP fixing all paths | Pjotr Prins | |
| 2016-04-20 | Successful startup of GN2 with MySQL | pjotrp | |
| 2016-04-20 | Remover dependency to logger_tree (may reintroduce later) | pjotrp | |
| 2016-04-20 | [PATCH 018/100] Find external tools: refactored code to work with GNU Guix | Pjotr Prins | |
| 2016-04-20 | README: add URL | pjotrp | |
| 2016-04-20 | * bin/genenetwork2: path handling | pjotrp | |
| 2016-04-20 | Removed import htmlgen as is not used (apparently) | pjotrp | |
| 2016-04-20 | * ./bin/genenetwork2: New file | pjotrp | |
| 2016-04-20 | Docs: Use ./doc dir instead of ./misc | pjotrp | |
| 2016-04-20 | [PATCH 012/100] Adding configuration for running a default server | Pjotr Prins | |
| 2016-04-20 | [PATCH 010/100] README | Pjotr Prins | |
| 2016-04-20 | Docs | Pjotr Prins | |
| 2016-04-19 | Merge branch 'master' of github.com:genenetwork/genenetwork2 into development | zsloan | |
| Conflicts: wqflask/base/trait.py | |||
| 2016-04-18 | Additive effect lines are now separated by chromosome (like the qtl line in ↵ | zsloan | |
| the last commit) Fixed order of stats table in trait page Removed the qtl results table from chromosome view; will add the Interval Analyst output later | |||
| 2016-04-14 | Fixed issue where qtl lines in interval mapping wouldn't connect between ↵ | zsloan | |
| chromosomes Added text explaining what * indicates in the mapping options menu Removed ranges (log2 and fold) from stats table for phenotype traits | |||
| 2016-04-13 | Moved the code getting the description/location because it was throwing an ↵ | zsloan | |
| error for phenotype traits | |||
| 2016-04-13 | Global search should be able to return description and location columns now | zsloan | |
| 2016-04-13 | All the datatables stuff should be passable by AJAX now, just need to figure ↵ | zsloan | |
| out how | |||
| 2016-04-12 | Fixed order of columns in AJAX-loading global search and added trait link | zsloan | |
| Table width is now correct with Y scrolling | |||
| 2016-04-11 | Changing global gene search to use gsearch_gene.html instead of ↵ | zsloan | |
| gsearch_gene_update.html | |||
| 2016-04-11 | Figured out how to load results into dataTable using AJAX, but still need to ↵ | zsloan | |
| get it working with Scroller correctly Added code getting the description, etc to trait.py since it was missed from last commit | |||
| 2016-04-11 | Changed the way trait data is retrieved for the global search page (it now ↵ | zsloan | |
| gets the LRS location repr and other variables needed to display in table during the retrieve_info function in trait.py instead of retrieve_trait_info in dataset.py) 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 | |||
| 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 ↵ | zsloan | |
| mapping scale (lrs or lod) Fixed bug where broken image link would appear if you ran R/qtl with no permutations | |||
| 2016-04-07 | SNP Track option should now work for GN1 mapping figure | zsloan | |
| Fixed typo in show_trait html that caused the p-value slider to not work for correlations | |||
| 2016-04-06 | The option to switch between LRS and LOD for the GN1 mapping figure should ↵ | zsloan | |
| now work correctly. 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) | |||
| 2016-04-06 | Setting lodm to always be 1.0 fixes the issue where it would incorrectly ↵ | zsloan | |
| display LOD scores for the Y-Axis instead of LRS values | |||
| 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 | Merge branch 'development' of github.com:genenetwork/genenetwork2 | zsloan | |
| 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) | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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