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ordering phenotype results from searches
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avoid having to restart each time a new dataset is added. Will need to keep an eye out for any issues, but doesn't seem to affect speed much
Fixed logic for UniProt link to use UniProtId instead of protein ID
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Phenotypes name when there's no accession ID
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correctly in certain situations
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Added option to download as JPEG in addition to SVG for basic stats figures
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Added a couple new third party links
Added link to GN1 trait page in trait pages
Fixed gene global search table appearance
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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
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Added some information to the mapping loading page
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json file
Removed option to edit certain html pages, like news, policies, etc
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Changed text in several pages (submit trait, mapping error)
Changed header menu structure some
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work for that now)
Fixed position digits and row highlighting on interval analyst table
Updated default MAF to 0.05
Updated footer text
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Fixed links to dataset info pages in search results and correlation results pages
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implementation of the reaper Dataset object doesn't include the addinterval method (so for those situations I still use reaper)
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)
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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
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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)
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Fixed a bug that sometimes occurred in search results
Changed order of items on index page
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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
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Made the outlier notification appear for all mapping methods
Removed some misleading text saying "Block samples" from the Transform and Filter Data section
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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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instead of integers)
Fixed error that caused N to show up as "null" in the trait sample table instead of "x"
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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
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other functions
Added the collection page features (correlation matrix, network graph, third party link-outs, etc) to the search result and correlation result pages
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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
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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
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chart if results exceed some number (5000 on GN1)
- 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"
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- 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
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just clicking their row in collection
- 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")
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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
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sample data into ElasticSearch
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)
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set width
Changed to using BIMBAM files to build Marker objects in dataset.py
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missing before
Removed a bunch of unused coded from all correlation-related files and the ctl analysis code
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pretty sure also isn't used any more.
Also removed some other unused code from the files listed
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in later when other third party links are implemented on the trait/collection pages
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Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
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* End the 'def' statement with a colon (:)
* Add an empty line between lines at different indentation levels for
clarity.
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with Plotly
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
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file format
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)
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for mapping
- 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
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appearance for mRNA assay data sets (still need to improve it for others)
Fixed minor logic issue in trait.py
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* 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
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