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2019-02-13Removed pylmm references and related functionsPjotr Prins
2019-02-13Remove all coffee filesPjotr Prins
2019-02-12Added GeneWeaver linkoutzsloan
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
2019-02-05Removed redundant header text from search page to save vertical spacezsloan
2019-02-05Fixed issue with getting marker info that affected heatmap and possibly ↵zsloan
other functions Added the collection page features (correlation matrix, network graph, third party link-outs, etc) to the search result and correlation result pages
2019-02-04Changed the way the table is drawn for the search pages so that it can show ↵zsloan
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)
2019-01-22Fixed issue where Haplotype Analyst in mapping results would always show ↵zsloan
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
2019-01-17Redid gene global search to take JSON data input instead of converting an ↵zsloan
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
2019-01-16Pushing SNP browser updateszsloan
2019-01-11Got InDel working for Variant Browserzsloan
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
2018-12-21Fixed collections so they can be very large (1000+ traits)zsloan
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
2018-12-05Fixed Verify linkzsloan
2018-12-05Fixed issue where SNP track for mapping did not appear correctlyzsloan
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
2018-11-20Added option to select chromosome from trait page when mappingzsloan
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
2018-11-13Changed trait sample table appearance to be more compactzsloan
2018-11-12Added change to remove qtlreaper use from correlation and prevent the ↵zsloan
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) :
2018-11-05Fixed quantile normalization issuezsloan
2018-11-04Fixed one more thingzsloan
2018-11-04Quick fix to issue where GEMMA wouldn't be run simultaneously on traits from ↵zsloan
the same group
2018-11-02Minor fix since sometimes number of samples with values wasn't counted correctlyzsloan
2018-11-02Committing some changes that get non-LOCO GEMMA mapping working without ↵zsloan
using precomputed kinship matrix
2018-11-01Updated the way snpbrowser initializes parameters, in preparation for ↵zsloan
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
2018-10-24- SNP Browser is mostly complete; just need to test more and add SNP density ↵zsloan
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"
2018-10-12Fixed issue that caused error when mapping single-chromosome, since a second ↵zsloan
reference to probeSetSearch wasn't removed
2018-10-11- Added fix for GEMMA LOCOzsloan
- 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
2018-10-01Missed something when previously resolving the merge conflictzsloan
2018-10-01Resolved conflictzsloan
2018-10-01- Can now remove cofactors from correlation scatterplot and select them by ↵zsloan
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")
2018-09-15Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingPjotr Prins
2018-09-15Run gemma without debug and checks in productionPjotr Prins
2018-08-15The issue with adding anonymous collections should be fixed nowzsloan
2018-08-14Fixed minor issue in user_manager.pyzsloan
2018-08-14Added cofactors to correlation scatterplot and changed it to use Plotlyzsloan
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
2018-07-06Added square root transform optionszsloan
Figures now correctly rescale when transforms are applied Fixed height of probability plot Removed some text related to pylmm since it's currently not being used
2018-07-02Added option to transform/normalize trait sample values (log2 and qnorm) on ↵zsloan
trait page Got figures mostly working with transformed values, except for changing the y-axis range of one Fixed issue with the home page "Make Default" button position (as well as the drop-downs in general) Added timeout to Elasticsearch connection to fix related error
2018-06-08Added option to add traits to existing collection, which I had forgotten ↵zsloan
previously
2018-06-08User collections (now stored in ElasticSearch) are reimplemented now and ↵zsloan
should have their full functionality back (adding/removing collections, adding/removing traits, etc)
2018-05-25Fixed issue causing anonymous collections to not work on my branch and ↵zsloan
staging, though still not sure why it's working on production without that change Added script to convert the dryad format genotype files to BIMBAM removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable
2018-05-17Added script to quantile normalize a data set and enter its normalized ↵zsloan
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)
2018-05-01Merge /home/lei/gene into testingzsloan
2018-05-01Removed all code related to using GEMMA with PLINK input fileszsloan
2018-04-27Added marker filtering for data set groups with larger genotype fileszsloan
Fixed issue where GEMMA + LOCO wasn't working with AIL (and probably some other groups)
2018-04-23Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a parameter ↵zsloan
instead of -lmm 1 (Wald test) Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py)
2018-04-19Changed width of top bar and a couple other html objects to 100% instead of ↵zsloan
set width Changed to using BIMBAM files to build Marker objects in dataset.py
2018-04-18Removed a little more code in webqtlDatabaseFunction.py and do_searchzsloan
2018-04-16Undoing changes to user_manager.py, because I think they may have caused ↵zsloan
some problem. Probably better to leave this file alone for the time being.
2018-04-16Resolved conflicts after pulling changeszsloan
2018-04-16Removed some unused code from collect.py and user_manager.pyzsloan
2018-04-16Removed file tracer.py that wasn't being usedzsloan
Removed some unused code from the other files listed
2018-04-16Removed a bunch of unused code from the following files:zsloan
marker_regression_gn1.py marker_regression.py do_search.py export_traits.py heatmap.py GeneUtil.py heatmap.html
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