| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2019-05-07 | Fixed issue where, if the user searched for a location range in the SNP ↵ | zsloan | |
| Browser, it often wouldn't correctly identify when markers were on genes | |||
| 2019-05-06 | Removed horizontal scroll from twitter field on index page | zsloan | |
| 2019-05-06 | Added link to Affiliates section of index page | zsloan | |
| 2019-05-06 | Made some changes Rob asked for to index page; reorganized some items and ↵ | zsloan | |
| made news scrollable | |||
| 2019-05-06 | Removed some unused imports of htmlgen | zsloan | |
| Fixed a bug that sometimes occurred in search results Changed order of items on index page | |||
| 2019-04-26 | Issue where GEMMA LOCO mapping didn't work when samples were edited out ↵ | zsloan | |
| should be fixed now | |||
| 2019-04-26 | Fixed issue where changed smaple values didn't show up in haplotype analyst ↵ | zsloan | |
| results | |||
| 2019-04-18 | Fixed issue that caused removed strains to still appear in the haplotype ↵ | zsloan | |
| analyst track | |||
| 2019-04-12 | Fixed PDF links in reference to point to the PDFs in GN1 | zsloan | |
| 2019-04-12 | - Improved Interval Analyst table appearance in mapping results | zsloan | |
| - Made the text on the "Forgot Password" page more simple and less cluttered - Added line to index page about RANGE search function - Fixed bar chart on trait page so that it sets the bottom margin depending upon the longest sample name length | |||
| 2019-04-10 | Removed option to upload file for submitting traits, since it doesn't ↵ | zsloan | |
| currently work | |||
| 2019-04-10 | Fixed issue that was causing submitted temp traits to not work | zsloan | |
| 2019-04-05 | Fixed issue that caused error for phenotype searches (kind of a quick fix ↵ | zsloan | |
| and I do a try/except for whether it can build the trait object; ideally I should correctly filter out datasets) | |||
| 2019-04-05 | Fixed issue where Max LRS column displayed the mean in global search results | zsloan | |
| 2019-04-04 | Fixed issue where dataset_menu_structure.json included some groups with no ↵ | zsloan | |
| visible datasets | |||
| 2019-04-03 | Fixed an issue that caused global phenotype search to often not work and ↵ | zsloan | |
| certain phenotype datasets to not show up in drop-downs | |||
| 2019-04-03 | Fixed issue where strains could be added twice in the SNP browser, causing ↵ | zsloan | |
| some wonky behavior | |||
| 2019-04-02 | Fixed issue where non-GEMMA mapping would throw an error because it would ↵ | zsloan | |
| still look for the results filename | |||
| 2019-03-29 | Fixed issue that caused PCA results to be different in GN2 than in GN1; one ↵ | zsloan | |
| result needed to be transposed | |||
| 2019-03-29 | Updated UCSC Verify link-out from hg19 to hg38 for humans | zsloan | |
| 2019-03-28 | Added link to GN2 document github wiki to index page | zsloan | |
| 2019-03-28 | Possibly fixed issue where PCA traits didn't calculate for certain sets of ↵ | zsloan | |
| traits | |||
| 2019-03-27 | Changed gen_select_dataset.py to be able to show multiple datasets under the ↵ | zsloan | |
| Phenotype type (for example the GI Tract Metabolome data) Fixed issue where full description was given for some unpublished traits Fixed code related to editing certain pages (like news) with CKEditor, but it still won't work until the CKEditor library is included in GUIX or something | |||
| 2019-03-25 | - Added SVG export to basic stats figures | zsloan | |
| - Fixed issues where some stats figures (mainly box and violin plots) didn't update correctly when sample values were changes - Fixed issue with some temp traits if user wasn't logged in - Fixed issue where traits couldn't be added to a collection from the correlation results page | |||
| 2019-03-19 | Added option to add PCA traits to collection from correlation matrix page | zsloan | |
| 2019-03-18 | - Added PCA traits to correlation matrix. You can't change their names yet ↵ | zsloan | |
| or add them to a collection from the corr matrix page, but you can click them and access them from the trait page. I'll add the option to access them from the corr matrix page as well, but adding the option to change their names might be trickier since they're currently used as their Redis keys. I need some better way of passing the Redis key around so it can be stored in collections, but this is tricky without changing the structure in ElasticSearch - Fixed the way temp traits work so you can use them with various functions, like mapping, correlations, network graph, etc - Fixed some appearance issue where the network graph options were too wide if a trait name was too long | |||
| 2019-03-13 | Zooming into chromosome or remapping with GEMMA is now very fast, since it ↵ | zsloan | |
| stores the output file Added option to search for terms in quotes, searching for all the contents within the quotes Added link to R/qtl documentation when user is in the R/qtl mapping tab | |||
| 2019-03-11 | Changed header style, because the jumbotrons previously used didn't look ↵ | zsloan | |
| that good. Now it's just a simple header element. | |||
| 2019-03-11 | Added default empty collection when user is logged in and attempts to add ↵ | zsloan | |
| traits to a collection Fixed issue with displaying cofactor selection tables for scatterplot Removed limit on text length for collection trait fields (dataset name and description) | |||
| 2019-03-07 | Changed the way covariates are displayed when selected for mapping | zsloan | |
| Made the outlier notification appear for all mapping methods Removed some misleading text saying "Block samples" from the Transform and Filter Data section | |||
| 2019-03-07 | Made violin plots for different groups/sample-sets different colors and ↵ | zsloan | |
| matched colors between box and violin plots | |||
| 2019-03-07 | Fixed issue where pressing enter in the search page text area would go to a ↵ | zsloan | |
| new line before submitting Also removed some pointless wrapper from dataset_select_menu_orig.js that was left over from being converted from coffeescript (need to do this with other files also) | |||
| 2019-03-07 | Fixed issue where correlation results containing NaN results sorted incorrectly | zsloan | |
| Set default permutations for R/qtl to 200 | |||
| 2019-03-06 | Cofactor option for correlation scatterplot was broken; it should be fixed now | zsloan | |
| Added title to basic stats table and made link for Interquartile Range more obvious Removed pointless "Delete Collection" button from correlation results page | |||
| 2019-03-05 | Made R/qtl metho/model names better and added some javascript to disable ↵ | zsloan | |
| wrong combinations of options | |||
| 2019-03-04 | Fixed excel export to show all columns | zsloan | |
| Fixed stats table to calculate Range and Interquartile Range correctly, and only show Range (fold) for appropriate traits | |||
| 2019-03-04 | - Added z-score transformation | zsloan | |
| - Added text indicating which transformation has been applied | |||
| 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 ↵ | zsloan | |
| separate one like I did for correlation previously Fixed some wrong text on heatmap page | |||
| 2019-03-01 | Added more information to the top-right corner of the mapping results | zsloan | |
| Fixed sorting issues on correlation page | |||
| 2019-02-27 | Added loading page for correlation | zsloan | |
| 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 | |||
| 2019-02-22 | Fixed some appearance issues with several tables | zsloan | |
| 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 | |||
| 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 ↵ | zsloan | |
| instead of integers) Fixed error that caused N to show up as "null" in the trait sample table instead of "x" | |||
| 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 | zsloan | |
| Also fixed such that sorting works with user-updated values | |||
| 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 | zsloan | |
| 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 | |||
| 2019-02-05 | Removed redundant header text from search page to save vertical space | zsloan | |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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