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Set default permutations for R/qtl to 200
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Added title to basic stats table and made link for Interquartile Range more obvious
Removed pointless "Delete Collection" button from correlation results page
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wrong combinations of options
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Fixed stats table to calculate Range and Interquartile Range correctly, and only show Range (fold) for appropriate traits
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- Added text indicating which transformation has been applied
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separate one like I did for correlation previously
Fixed some wrong text on heatmap page
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Fixed sorting issues on correlation page
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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
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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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Updated instructions and SERVER_PORT for single flask server
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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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Also fixed such that sorting works with user-updated values
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Gn testing: updates to scripts, removed coffee scripts and removed pylmm code
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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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when loading and more easily control cell contents
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)
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results from Chromosome 1
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
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HTML table, and adding loading text
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
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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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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
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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
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inconsistent error
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)
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the same group
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using precomputed kinship matrix
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drawing SNP density chart when results exceed a certain value, plus a couple minor fixes
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
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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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Forgot to add to change user to root during the last commit
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Since I know I'll forget otherwise, updated instructions on starting up ES
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reference to probeSetSearch wasn't removed
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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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