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2019-05-24Added currently api progress, which will henceforth be appropriately ↵zsloan
committed in this branch
2019-05-24Replaced qtlreaper Dataset object with python objectzsloan
2019-05-23Fixed issue where some descriptions caused an errorzsloan
2019-05-17Made check for trait IDs a bit more secure to hopefully avoid any errors ↵zsloan
similar to the previous one with a missing unigene id
2019-05-17Fixed issue that caused error for traits with no unigene idzsloan
2019-05-14Added all of the third party links from GN1zsloan
Fixed issue with the script that generates the drop-down menus where phenotype/genotype datasets wouldn't show up for species without any mRNA assay datasets Added icon for smartphones/tablets Made error more informative for main search Added gene symbol column to collections (need to add something that removes the column if it's all empty)
2019-05-08Fixed issue where descriptions sometimes had unicode characters appear strangelyzsloan
2019-05-07Added link to GeneBridge to trait pagezsloan
2019-05-07Fixed 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
2019-05-06Removed horizontal scroll from twitter field on index pagezsloan
2019-05-06Added link to Affiliates section of index pagezsloan
2019-05-06Made some changes Rob asked for to index page; reorganized some items and ↵zsloan
made news scrollable
2019-05-06Removed some unused imports of htmlgenzsloan
Fixed a bug that sometimes occurred in search results Changed order of items on index page
2019-04-26Issue where GEMMA LOCO mapping didn't work when samples were edited out ↵zsloan
should be fixed now
2019-04-26Fixed issue where changed smaple values didn't show up in haplotype analyst ↵zsloan
results
2019-04-18Fixed issue that caused removed strains to still appear in the haplotype ↵zsloan
analyst track
2019-04-12Fixed PDF links in reference to point to the PDFs in GN1zsloan
2019-04-12- Improved Interval Analyst table appearance in mapping resultszsloan
- 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
2019-04-10Removed option to upload file for submitting traits, since it doesn't ↵zsloan
currently work
2019-04-10Fixed issue that was causing submitted temp traits to not workzsloan
2019-04-05Fixed 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)
2019-04-05Fixed issue where Max LRS column displayed the mean in global search resultszsloan
2019-04-04Fixed issue where dataset_menu_structure.json included some groups with no ↵zsloan
visible datasets
2019-04-03Fixed an issue that caused global phenotype search to often not work and ↵zsloan
certain phenotype datasets to not show up in drop-downs
2019-04-03Fixed issue where strains could be added twice in the SNP browser, causing ↵zsloan
some wonky behavior
2019-04-02Fixed issue where non-GEMMA mapping would throw an error because it would ↵zsloan
still look for the results filename
2019-03-29Fixed issue that caused PCA results to be different in GN2 than in GN1; one ↵zsloan
result needed to be transposed
2019-03-29Updated UCSC Verify link-out from hg19 to hg38 for humanszsloan
2019-03-28Added link to GN2 document github wiki to index pagezsloan
2019-03-28Possibly fixed issue where PCA traits didn't calculate for certain sets of ↵zsloan
traits
2019-03-27Changed 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 figureszsloan
- 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
2019-03-19Added option to add PCA traits to collection from correlation matrix pagezsloan
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
2019-03-13Zooming 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
2019-03-11Changed header style, because the jumbotrons previously used didn't look ↵zsloan
that good. Now it's just a simple header element.
2019-03-11Added 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)
2019-03-07Changed the way covariates are displayed when selected for mappingzsloan
Made the outlier notification appear for all mapping methods Removed some misleading text saying "Block samples" from the Transform and Filter Data section
2019-03-07Made violin plots for different groups/sample-sets different colors and ↵zsloan
matched colors between box and violin plots
2019-03-07Fixed 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)
2019-03-07Fixed issue where correlation results containing NaN results sorted incorrectlyzsloan
Set default permutations for R/qtl to 200
2019-03-06Cofactor option for correlation scatterplot was broken; it should be fixed nowzsloan
Added title to basic stats table and made link for Interquartile Range more obvious Removed pointless "Delete Collection" button from correlation results page
2019-03-05Made R/qtl metho/model names better and added some javascript to disable ↵zsloan
wrong combinations of options
2019-03-04Fixed excel export to show all columnszsloan
Fixed stats table to calculate Range and Interquartile Range correctly, and only show Range (fold) for appropriate traits
2019-03-04- Added z-score transformationzsloan
- Added text indicating which transformation has been applied
2019-03-01Added alternating point colors for manhattan plotszsloan
2019-03-01Changed 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
2019-03-01Added more information to the top-right corner of the mapping resultszsloan
Fixed sorting issues on correlation page
2019-02-27Added loading page for correlationzsloan
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
2019-02-22Fixed some appearance issues with several tableszsloan
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
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