genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2019-03-04	Fixed excel export to show all columns	zsloan
	Fixed stats table to calculate Range and Interquartile Range correctly, and only show Range (fold) for appropriate traits
2019-03-04	- Added z-score transformation	zsloan
	- Added text indicating which transformation has been applied
2019-03-01	Added alternating point colors for manhattan plots	zsloan

2019-03-01	Changed 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
2019-03-01	Added more information to the top-right corner of the mapping results	zsloan
	Fixed sorting issues on correlation page
2019-02-27	Added loading page for correlation	zsloan
	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
2019-02-22	Fixed some appearance issues with several tables	zsloan
	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
2019-02-18	Updated installation instructions and SERVER_PORT for single flask server	Pjotr Prins

2019-02-15	Fixed error caused by change to N values in database (now takes strings ↵	zsloan
	instead of integers) Fixed error that caused N to show up as "null" in the trait sample table instead of "x"
2019-02-14	Fixed minor bug with updating stats figures when sample values changed	zsloan

2019-02-14	Changed trait page tables to load JSON	zsloan
	Also fixed such that sorting works with user-updated values
2019-02-13	Removed pylmm references and related functions	Pjotr Prins

2019-02-13	Remove all coffee files	Pjotr Prins

2019-02-12	Added GeneWeaver linkout	zsloan
	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
2019-02-05	Removed redundant header text from search page to save vertical space	zsloan

2019-02-05	Fixed 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
2019-02-04	Changed 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)
2019-01-22	Fixed 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
2019-01-17	Redid 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
2019-01-16	Pushing SNP browser updates	zsloan

2019-01-11	Got InDel working for Variant Browser	zsloan
	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
2018-12-21	Fixed 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
2018-12-05	Fixed Verify link	zsloan

2018-12-05	Fixed issue where SNP track for mapping did not appear correctly	zsloan
	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
2018-11-20	Added option to select chromosome from trait page when mapping	zsloan
	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
2018-11-13	Changed trait sample table appearance to be more compact	zsloan

2018-11-12	Added 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) :
2018-11-05	Fixed quantile normalization issue	zsloan

2018-11-04	Fixed one more thing	zsloan

2018-11-04	Quick fix to issue where GEMMA wouldn't be run simultaneously on traits from ↵	zsloan
	the same group
2018-11-02	Minor fix since sometimes number of samples with values wasn't counted correctly	zsloan

2018-11-02	Committing some changes that get non-LOCO GEMMA mapping working without ↵	zsloan
	using precomputed kinship matrix
2018-11-01	Updated 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"
2018-10-12	Fixed 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 LOCO	zsloan
	- 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
2018-10-01	Missed something when previously resolving the merge conflict	zsloan

2018-10-01	Resolved conflict	zsloan

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")
2018-09-15	Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing	Pjotr Prins

2018-09-15	Run gemma without debug and checks in production	Pjotr Prins

2018-08-15	The issue with adding anonymous collections should be fixed now	zsloan

2018-08-14	Fixed minor issue in user_manager.py	zsloan

2018-08-14	Added cofactors to correlation scatterplot and changed it to use Plotly	zsloan
	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
2018-07-06	Added square root transform options	zsloan
	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
2018-07-02	Added 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
2018-06-08	Added option to add traits to existing collection, which I had forgotten ↵	zsloan
	previously
2018-06-08	User collections (now stored in ElasticSearch) are reimplemented now and ↵	zsloan
	should have their full functionality back (adding/removing collections, adding/removing traits, etc)
2018-05-25	Fixed 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
2018-05-17	Added 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)