| Age | Commit message (Expand) | Author |
|---|
| 2019-03-07 | Fixed issue where correlation results containing NaN results sorted incorrectly...Set default permutations for R/qtl to 200
| zsloan |
| 2019-03-06 | Cofactor option for correlation scatterplot was broken; it should be fixed now...Added title to basic stats table and made link for Interquartile Range more obvious
Removed pointless "Delete Collection" button from correlation results page
| zsloan |
| 2019-03-05 | Made R/qtl metho/model names better and added some javascript to disable wron... | zsloan |
| 2019-03-04 | Fixed excel export to show all columns...Fixed stats table to calculate Range and Interquartile Range correctly, and only show Range (fold) for appropriate traits
| zsloan |
| 2019-03-04 | - Added z-score transformation...- Added text indicating which transformation has been applied
| zsloan |
| 2019-03-01 | Added alternating point colors for manhattan plots | zsloan |
| 2019-03-01 | Changed loading page to work for any feature, instead of having to make a sep......Fixed some wrong text on heatmap page
| zsloan |
| 2019-03-01 | Added more information to the top-right corner of the mapping results...Fixed sorting issues on correlation page
| zsloan |
| 2019-02-27 | Added loading page for correlation...Added a better error page for mapping if no results are returned (which generally implied an error occurred during the running of GEMMA)
Fixed some issues with tables, like them sorting incorrectly or showing the wrong number of digits
| zsloan |
| 2019-02-22 | Fixed some appearance issues with several tables...Fixed issue where cofactor selection screens were broken
Changed case attributes to be applied across groups, though need to discuss this with Rob since it shouldn't always be done this way
Added new inversion transformation
| zsloan |
| 2019-02-18 | Updated installation instructions and SERVER_PORT for single flask server | Pjotr Prins |
| 2019-02-15 | Fixed error caused by change to N values in database (now takes strings inste......Fixed error that caused N to show up as "null" in the trait sample table instead of "x"
| zsloan |
| 2019-02-14 | Fixed minor bug with updating stats figures when sample values changed | zsloan |
| 2019-02-14 | Changed trait page tables to load JSON...Also fixed such that sorting works with user-updated values
| zsloan |
| 2019-02-13 | Removed pylmm references and related functions | Pjotr Prins |
| 2019-02-13 | Remove all coffee files | Pjotr Prins |
| 2019-02-12 | Added GeneWeaver linkout...Fixed some issues with sorting in various tables
Changed header appearance for some pages
Fixed bug where basic stats table would sometimes be duplicated or show up with empty fields
| zsloan |
| 2019-02-05 | Removed redundant header text from search page to save vertical space | zsloan |
| 2019-02-05 | Fixed issue with getting marker info that affected heatmap and possibly other......Added the collection page features (correlation matrix, network graph, third party link-outs, etc) to the search result and correlation result pages
| zsloan |
| 2019-02-04 | Changed the way the table is drawn for the search pages so that it can show w......Added typeahead to snp_browser (still need to tell it only to use it for rat, though)
Added WebGestalt link to collection page (still need to add it and BNW to other trait list pages)
| zsloan |
| 2019-01-22 | Fixed issue where Haplotype Analyst in mapping results would always show resu......Fixed issue where traits couldn't be added to a collection from the global search results
Made some improvements to the gene global search table
| zsloan |
| 2019-01-17 | Redid gene global search to take JSON data input instead of converting an HTM......Made some changes to make trait page SNPs link point to GN2 SNP Browser, as well as make other links open in new tabs/windows
| zsloan |
| 2019-01-16 | Pushing SNP browser updates | zsloan |
| 2019-01-11 | Got InDel working for Variant Browser...Changed Variant Browser to display gene name under "Domain" when the user searches a gene term and rows are mislabeled "Intergenic"
Fixed Chr option to display correct chromosomes for different species
Fixed order for correlation drop-down on trait page
Fixed some appearance issues with the mapping results table
Improved appearance of correlation scatterplot page
| zsloan |
| 2018-12-21 | Fixed collections so they can be very large (1000+ traits)...Added option to submit traits in collection to BNW
Fixed issue with "x" values for user-submitted traits
Fixed issue where post-publications descriptions were wrongly appearing in global search results
| zsloan |
| 2018-12-05 | Fixed Verify link | zsloan |
| 2018-12-05 | Fixed issue where SNP track for mapping did not appear correctly...Updated style for a variety of tables
Moved transform/blocking tools for trait sample table into its own tab
Added some new customization options to network graph
Started work on implementing third party link-outs
Updated drop-down generation script to order datasets according to CreateTime
| zsloan |
| 2018-11-20 | Added option to select chromosome from trait page when mapping...Put transform/blocking tools into their own tab (still need to change formatting of tab's contents)
Improved appearance of search result page table (still need to change a few other tables)
Fixed issue that caused parent/f1 strains to not be blocked correctly when using "block by index" tool
Basic Stats figures now load when the user clicks the tab, to improve initial page load time
| zsloan |
| 2018-11-13 | Changed trait sample table appearance to be more compact | zsloan |
| 2018-11-12 | Added change to remove qtlreaper use from correlation and prevent the inconsi......Added change to change maf depending upon number of sample values
Committing in-process changes to how sample table is built on trait page (to make it look better and more compact)
:
| zsloan |
| 2018-11-05 | Fixed quantile normalization issue | zsloan |
| 2018-11-04 | Fixed one more thing | zsloan |
| 2018-11-04 | Quick fix to issue where GEMMA wouldn't be run simultaneously on traits from ... | zsloan |
| 2018-11-02 | Minor fix since sometimes number of samples with values wasn't counted correctly | zsloan |
| 2018-11-02 | Committing some changes that get non-LOCO GEMMA mapping working without using... | zsloan |
| 2018-11-01 | Updated the way snpbrowser initializes parameters, in preparation for drawing......Changed the header bar to put a few items under the "Help" option, since previously the header was too long and would go to a second line when the browser window width was smaller
Changed dataset info link on trait page to same as one on search page
Changed the mapping default to non-LOCO for the time being, until it is faster
| zsloan |
| 2018-10-24 | - SNP Browser is mostly complete; just need to test more and add SNP density ......- Removed unnecessary options from the mode bar for the trait page Plotly figures and changed the default to highlight points the mouse is hovering over
- Changed some file/function names related to mapping, which previously were erroneously named "marker_regression"
| zsloan |
| 2018-10-12 | Fixed issue that caused error when mapping single-chromosome, since a second ... | zsloan |
| 2018-10-11 | - Added fix for GEMMA LOCO...- Added all current SNP browser code (not complete yet)
- Added change to convert_geno_to_bimbam that makes it ignore .geno files marked as "filler" (so ones where the .geno file is fake and we sometimes directly receive the genotypes as BIMBAM)
- Changes TheSpecies object in species.py to accept species name as well as dataset name
| zsloan |
| 2018-10-01 | Missed something when previously resolving the merge conflict | zsloan |
| 2018-10-01 | Resolved conflict | zsloan |
| 2018-10-01 | - Can now remove cofactors from correlation scatterplot and select them by ju......- Cofactor color picker now works in Safari/Macs
- Displays N for relevant samples in trait page sample table
- Don't show bar chart when N>256
- Mapping loading page contents better centered
- Anonymous collections timeout correctly listed as 30 days now
- Minor allele frequency can actually be changed for GEMMA now (previously didn't work)
- Fixed transcript position marker location for mapping results
- Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password
- Users can now map with submitted traits
- Histogram width changes depending upon number of bins (need to improve this still)
- Improved Q-q plot (previously called "probability plot")
| zsloan |
| 2018-09-15 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | Pjotr Prins |
| 2018-09-15 | Run gemma without debug and checks in production | Pjotr Prins |
| 2018-08-15 | The issue with adding anonymous collections should be fixed now | zsloan |
| 2018-08-14 | Fixed minor issue in user_manager.py | zsloan |
| 2018-08-14 | Added cofactors to correlation scatterplot and changed it to use Plotly...Added Phenogen track to mapping results
Added comparison bar chart figure
Simplified global search to not build trait/dataset objects, which speeds thing up considerably
Fixed correlation matrix to correctly deal with 0 values
Fixed issue where anonymous collections couldn't be created if none already existed
| zsloan |
| 2018-07-06 | Added square root transform options...Figures now correctly rescale when transforms are applied
Fixed height of probability plot
Removed some text related to pylmm since it's currently not being used
| zsloan |
| 2018-07-02 | Added option to transform/normalize trait sample values (log2 and qnorm) on t......Got figures mostly working with transformed values, except for changing the y-axis range of one
Fixed issue with the home page "Make Default" button position (as well as the drop-downs in general)
Added timeout to Elasticsearch connection to fix related error
| zsloan |
| 2018-06-08 | Added option to add traits to existing collection, which I had forgotten prev... | zsloan |
