| Age | Commit message (Expand) | Author |
|---|
| 2019-11-14 | Changed code to rebuild dataset list each time you view the trait page to avo......Fixed logic for UniProt link to use UniProtId instead of protein ID
| zsloan |
| 2019-11-05 | Fixed issue with ordering items in correlation dataset select dropdown | zsloan |
| 2019-10-24 | Changed logic for generating drop-downs such that it shows the correct Phenot... | zsloan |
| 2019-10-18 | Added UniProt link and fixed issue that caused sample lists to not be formed ... | zsloan |
| 2019-10-04 | Fixed issue where there was an error if the REST API used for aliases was down...Added option to download as JPEG in addition to SVG for basic stats figures
| zsloan |
| 2019-08-22 | Changed header drop-down menu layout...Added a couple new third party links
Added link to GN1 trait page in trait pages
Fixed gene global search table appearance
| zsloan |
| 2019-08-01 | Updated aliases to get all species aliases and remove duplicates | zsloan |
| 2019-08-01 | Added wikidata aliases...Fixed year to not be a hyperlink when no pubmed id
Fixed first column width so it doesn't go onto two lines for trait details
| zsloan |
| 2019-08-01 | Made some more aesthetic changes to various pages and charts/figures...Added some information to the mapping loading page
| zsloan |
| 2019-07-23 | Added change to automatically update datasets list using rest api instead of ......Removed option to edit certain html pages, like news, policies, etc
| zsloan |
| 2019-07-18 | Made change that should fix encoding issue, fingers crossed | zsloan |
| 2019-07-03 | Fixed bug for creating one of the third party links on the trait page...Changed text in several pages (submit trait, mapping error)
Changed header menu structure some
| zsloan |
| 2019-06-24 | Got non-LOCO GEMMA mapping working with gemma-wrapper (so caching should work......Fixed position digits and row highlighting on interval analyst table
Updated default MAF to 0.05
Updated footer text
| zsloan |
| 2019-06-18 | Fixed issue with sorting involving 0's on trait page...Fixed links to dataset info pages in search results and correlation results pages
| zsloan |
| 2019-06-05 | Fixed issue that caused interval mapping to not work because the python imple......Fixed issue where the last chromosome wasn't displayed for mapping results (though still need to fix issue where points are drawn too far to the right when a specific range is viewed)
| zsloan |
| 2019-06-04 | Added GeneMANIA link...Fixed issue that caused error when creating UCSC RefSeq link
Fixed issue that sometimes caused an error for phenotype searches
Changed some text on collections page
| zsloan |
| 2019-05-24 | Replaced qtlreaper Dataset object with python object | zsloan |
| 2019-05-14 | Added all of the third party links from GN1...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)
| zsloan |
| 2019-05-06 | Removed some unused imports of htmlgen...Fixed a bug that sometimes occurred in search results
Changed order of items on index page
| zsloan |
| 2019-03-18 | - Added PCA traits to correlation matrix. You can't change their names yet or......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
| zsloan |
| 2019-03-07 | Changed the way covariates are displayed when selected for mapping...Made the outlier notification appear for all mapping methods
Removed some misleading text saying "Block samples" from the Transform and Filter Data section
| 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 |
| 2019-02-15 | 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 |
| 2019-02-13 | Removed pylmm references and related functions | 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 | 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 |
| 2019-01-11 | 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 |
| 2018-10-24 | - 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 |
| 2018-10-11 | - 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 | - 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 |
| 2018-08-14 | 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 |
| 2018-05-17 | Added script to quantile normalize a data set and enter its normalized sample......Added option to replace trait page sample/strain values with normalized ones
Began editing Lei's scatterplot code
Changed elasticsearch_tools' get_elasticsearch_connection so that it can also be used for purposes other than user authentication (by adding a "for_user" parameter)
| zsloan |
| 2018-04-19 | Changed width of top bar and a couple other html objects to 100% instead of s......Changed to using BIMBAM files to build Marker objects in dataset.py
| zsloan |
| 2018-04-16 | Resolved conflicts after pulling changes | zsloan |
| 2018-04-11 | Added tissue correlation p value to correlation page results, since it was mi......Removed a bunch of unused coded from all correlation-related files and the ctl analysis code
| zsloan |
| 2018-04-09 | Removed svg.py, which I know isn't used, and webqtlFormData, which I'm pretty......Also removed some other unused code from the files listed
| zsloan |
| 2018-04-09 | Removed unused code from webqtlFormData.py | zsloan |
| 2018-04-09 | Removed some unused code in webqtlConfig; some might need to be added back in... | zsloan |
| 2018-04-06 | Mapping figure output now gives more accurate information...Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
| zsloan |
| 2018-03-22 | Fix 'def' statement...* End the 'def' statement with a colon (:)
* Add an empty line between lines at different indentation levels for
clarity.
| Muriithi Frederick Muriuki |
| 2018-02-10 | Check for bimbam path and bail out if it is missing | Pjotr Prins |
| 2017-12-20 | Bring in some earlier work - mostly documentation and startup handling | Pjotr Prins |
| 2017-11-06 | Replaced Histogram and Bar Chart with Plotly version and added new Box Plot w......GEMMA now has option to select genotypes
Updated dataset select dropdowns to be ordered correctly
Fixed dataset select dropdowns for correlations to not show confidential datasets
Added Skewness and Kurtosis to Basic Statistics table
Fixed Verify and RNA-seq buttons on trait page
Temporarily hardcoded Reference page until we get it to link with database
| zsloan |
| 2017-08-29 | Mostly changes related to getting gemma working with covariates and BIMBAM fi......Other changes include:
- Fixing links in the network graph
- Changing button colors on show trait page
- Changing color scheme for heatmap
- Making rows highlight in yellow when clicked on
- Some changes to table appearance (like giving gene global search a horizontal scroll)
| zsloan |
| 2017-06-12 | Fixed issue where 0.0 values would be converted into X's on the trait page | zsloan |
| 2017-06-09 | - Changed the way the genofile is set so different genofiles can be selected ......- Now shows error page for Correlation Matrix if traits aren't all from the same group (later need to make it check for shared samples, since different groups may contain some of the same samples
- Mapping results page now displays the genofile in the information section
- Only show Interval Analyst if species is mouse or rat (previously it would show a blank table for other species)
- Network Graph now only shows links in a node's info if the relevant information (for example geneid) exists, and the label changes depending on the type of data set
- Other minor changes to the appearance of the Network Graph menu (less white space, plus clickable descriptions for a couple options)
- Improved Correlations Results page to shorten Description and Authors cell content for Phenotype traits (to keep table width manageable)
- Changed the glossary links for LRS and Additive Effect columns for Gene Global Search
- Improved appearance for Phenotype Global Search results
- Temporarily removed Mapping options/features that don't work from the trait page
| zsloan |
| 2017-05-31 | Added various tool options to correlation results page and improved table app......Fixed minor logic issue in trait.py
| zsloan |
| 2017-05-21 | Merge from the diet branch.... * refactored ./bin/genenetwork2 and /etc/default_settings
- better detection of Guix
- removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS
- removing some default settings, such as PYLMM_COMMAND
- rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY
- added GUIX_JS_PATH for JS modules
* Added documentation on installing binary GN2
* Updated Twitter board to latest version in Guix - it had broken
* Updated many tools in the latest Guix profile
| Pjotr Prins |
| 2017-04-17 | Added option to remove collections from collection list page...Improved appearance of search result and collection tables
| zsloan |
