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2021-09-13Change Genotype File text to only show the meaningful genotype deescriptionzsloan
2021-09-13Temporarily point the View in GN1 button to gn1-lily.genenetwork.org since ↵zsloan
some features aren't working on gn1.genenetwork.org yet
2021-09-11Add Jupyter Notebook Launcher to Tools dropdown menujgart
2021-09-10Fix issue with the way the template was checking if genofile_string was set; ↵zsloan
it was receiving an empty string, so the previous logic made it think there was a genofile string when there wasn't one
2021-09-10Removed encoding, since it's apparently not needed since the Python 3 ↵zsloan
switchover (and was causing there to be no matches between user IDs and groups)
2021-09-09Merge pull request #600 from zsloan/feature/add_more_mapping_metadatazsloan
Feature/add more mapping metadata
2021-09-09Change trait name to display name in the metadata at the top of the page (so ↵zsloan
group codes will be includes in phenotype IDs
2021-09-09Replaced trait name with trait display name in display_mapping_results so ↵zsloan
the group codes will be includes in phenotype IDs
2021-09-07Add trait hash and datetime to mapping figurezsloan
2021-09-07Add timer to loading page to track how long the process has been runningzsloan
2021-09-05Fixed issue that caused sample data to not be fetched correctly; there's ↵zsloan
something wrong with the 'get_probeset_data' function (not sure why this function exists)
2021-09-03Allow categorical_var_list to be passed as a template variablezsloan
2021-09-03Fix issue that caused javascript to not work on the R/qtl mapping result ↵zsloan
page when permutations weren't used (because it wrongly expected the permutation histogram to always exist)
2021-09-03Fix issue where values written to phenotype file for R/qtl sometimes had ↵zsloan
trailing decimal values by grounding to 3 places past the decimal
2021-08-27Fix pair_scan button to not submit twicezsloan
2021-08-26Fixed pair_scan to pairscan since that's what the parameter is when passed ↵zsloan
to gn3 and rqtl_wrapper.R
2021-08-26Add pair_scan default value to hddn params in show_trait.pyzsloan
2021-08-26Only store js_data if not using pair_scan (which doesn't need it) + remove ↵zsloan
unused code from the previous pair_scan implementation
2021-08-26Set pair_scan to true when pair_scan is usedzsloan
2021-08-26Changed the pair-scan template to work with the R/qtl pair-scan results and ↵zsloan
d3panels figure; still need to add table and permutation results
2021-08-26Fixed bug caused by pair_scan not always being set to a defaultzsloan
2021-08-26Store figure and table data for pair_scan in run_mapping.pyzsloan
2021-08-26Added pair_scan parameter to rqtl_mapping.run_rqtl and fixed setting ↵zsloan
mapmethod_rqtl and mapmodel_rqtl in run_mapping.py
2021-08-26Added defaults for mapmethod_rqtl and mapmodel_rqtl to show_trait.pyzsloan
2021-08-26Changed mapmethod/mapmodel variables names in mapping_results_page (the way ↵zsloan
these variables are passed is really dumb but I'm not sure how to better deal with the situation)
2021-08-26Fixed mapmethod/mapmodel variables names in mapping_input_listzsloan
2021-08-26Fixed some issues with the Pair Scan options and JSzsloan
2021-08-26Added JS for submitting pair scan from trait pagezsloan
2021-08-26Added Pair Scan options to the Mapping Tools tab in the trait pagezsloan
2021-08-26Added check for pair_scan in start_varszsloan
2021-08-25Fix issue where correlation results weren't included parents/f1szsloan
2021-08-25Fixed issue in get_diff_of_vals that caused the diff to be calculated wrong ↵zsloan
(due to one set of values being rounded to 3 digits and the other not
2021-08-25Add map scale option that was missing for groups with only a single genotype ↵zsloan
file
2021-08-25Fix issue that could cause an error when doing cM mappingzsloan
2021-08-25Fix issue that could cause mapping_scale to not be set correctly in ↵zsloan
show_trait.py
2021-08-24README: on installing GN2Pjotr Prins
2021-08-24README: minor editsPjotr Prins
2021-08-24README: install with guix profilePjotr Prins
2021-08-23Merge pull request #599 from zsloan/bug/fix_mapping_recompute_issuezsloan
Bug/fix mapping recompute issue
2021-08-23Removed unused variable from list of 'wanted' variables for mappingzsloan
2021-08-23Fixed issue with the way categorical_vars and perm_strata were being passed ↵zsloan
to the template
2021-08-23Account for situations where the minimum permutation value is also above ↵zsloan
webqtlConfig.MAXLRS; previously threw an error
2021-08-23Fix get_perm_strata to usethe Ids for case attributes instead of names + ↵zsloan
allow perm_strata to be passed to the template
2021-08-23Fix the way categorical_var_list is set to account for case attribute Ids ↵zsloan
being keys now instead of names
2021-08-23Include categorical_vars in mapping_results.html so they're included when ↵zsloan
recomputing
2021-08-23For some reason sample_data was being set twice, and the second time used a ↵zsloan
test function that does not exclude parents/f1s (causing the N to be wrong if parents/f1s exist)
2021-08-20Fixed some logic in trait.py that could cause a problem if a dataset_name ↵zsloan
was passed that wasn't Temp
2021-08-20Fix issue where attempting to get the diff of vals for Temp traits was ↵zsloan
causing an error
2021-08-20startup_config.py: Add DebugToobarExtension for wsgi DEBUG modeBonfaceKilz
* wqflask/utility/startup_config.py (app_config): Add DebugToolbarExtension
2021-08-19Change color for Submit button when selecting covariates + move Back button ↵zsloan
to the far right
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