| Age | Commit message (Expand) | Author |
|---|---|---|
| 2018-10-11 | - Added fix for GEMMA LOCO...- 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 | zsloan |
| 2018-10-01 | - Can now remove cofactors from correlation scatterplot and select them by ju......- 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") | zsloan |
| 2018-05-25 | Fixed issue causing anonymous collections to not work on my branch and stagin......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 | zsloan |
| 2018-05-17 | Added script to quantile normalize a data set and enter its normalized sample......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) | zsloan |
| 2018-04-23 | Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a parameter in......Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py) | zsloan |
| 2018-04-16 | Resolved conflicts after pulling changes | zsloan |
| 2018-04-12 | README and docs | Pjotr Prins |
| 2018-04-09 | Removed unused code from get_select_dataset.py and get_group_samplelists.py s... | zsloan |
| 2018-04-09 | Removed unused code from convert_geno_to_bimbam.py and corestats.py | zsloan |
| 2017-12-06 | Fixed drop-down group order | zsloan |
| 2017-12-04 | Fixed drop-down scripts to more appropriately deal with BXD300 groups (though......Added some header data to mapping output file Fixed links in Network Group nodes/edges | zsloan |
| 2017-11-06 | Replaced Histogram and Bar Chart with Plotly version and added new Box Plot w......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 | zsloan |
| 2017-09-07 | Added the script to convert bimbam to kinship matrices | zsloan |
| 2017-09-05 | Added file converting genofiles to bimbam | zsloan |
| 2017-05-21 | Merge from the diet branch.... * 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 | Pjotr Prins |
| 2017-02-08 | Changed the way .fam files are written/read, which fixes the issue with GEMMA... | zsloan |
| 2016-12-12 | Moved a bunch of functions out of the GeneralTrait class that didn't need to ......Improved loadings plot on the correlation matrix page to look like GN1's figure (though it's vector and GN1's was static) Removed some unused code from show_trait.py changed appearance of table headers some, though needs a little more work Updated dataset_menu_structure.json | zsloan |
| 2016-09-30 | Add missing __init__.py | Pjotr Prins |
| 2016-09-13 | Fixed the path for the json file in gen_select_dataset.py since it was wrong ......Added "Reset" option to network graph that returns all the nodes/edges Made the visualization options area in the network graph a little wider | zsloan |
| 2016-09-13 | Run scripts from ./wqflask - just like the webserver | Pjotr Prins |
| 2016-09-10 | Comment | Pjotr Prins |
| 2016-09-10 | Support for running maintenance scripts so they can pick up all webserver set......Run with ./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py | Pjotr Prins |
| 2016-07-16 | README: added info | Pjotr Prins |
| 2016-06-19 | Renamed settings so they are grouped together | Pjotr Prins |
| 2016-06-18 | Changed file permssions to non-executable | Pjotr Prins |
| 2016-06-18 | Disable setting sys.paths | Pjotr Prins |
| 2016-06-17 | Conflict | Pjotr Prins |
| 2016-06-17 | Removed trailing spaces in .py and .js files | Pjotr Prins |
| 2016-06-16 | Generating the menu is now obsolete | Pjotr Prins |
| 2016-04-20 | More hard-coded | pjotrp |
| 2016-04-20 | [PATCH 037/100] WebQtlConfig: sanitizing naming and used vars | Pjotr Prins |
| 2016-02-18 | Edited gen_select_dataset to remove confidential datasets...Also hard-coded the removal of Macaque Monkey since I couldn't think of a good way to retroactively check if every dataset in a species is confidential | zsloan |
| 2016-01-29 | Info button should now work for phenotype and genotype datasets | zsloan |
| 2016-01-27 | Merge branch 'master' of github.com:genenetwork/genenetwork2 into development | zsloan |
| 2016-01-27 | Added info button to Dataset dropdown on index page...Fixed script that generates dataset dropdown json file to include accession id Fixed dataset link on search results page | zsloan |
| 2016-01-26 | Removed a bunch of files/directories/packages that are no longer used and som... | zsloan |
| 2015-07-09 | Forgot to add one change to the last commit | zsloan |
| 2015-07-09 | Mapping methods now check for existing genotype files....Currently we still usually get our samplelists from the genofile. This is dumb because it results in us having a bunch of "dummy" genofiles for certain data sets (seems to be mostly human ones). This means that checking for the genofile alone isn't enough to determine if a mapping method should exist for a given group I wrote some code that will instead get the samplelist from the plink .fam file for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy .geno files, but we can't yet do so because it's currently the only place we seem to be storing the sample list for some groups. I also moved gemma into the plink directory to get it out of the git tree. Since it uses the same files as plink, it doesn't make sense for it to be in its own separate directory | zsloan |
| 2015-05-11 | Fixed gen_select_dataset so that it does not include Phenotype and...Genotype groups when the corresponding data sets do not exist Interval Mapping no longer shows up for human traits Fixed the appearance of the mirror links on the main page | zsloan |
| 2014-08-28 | Added a validation that warns the user of the number of permutations for...pyLMM is more than 20 (due to speed) Changed the port in the flask settings to 5002 due to adding the new production server branch | Zachary Sloan |
| 2014-07-14 | Merge /home/zas1024/gene...Conflicts: wqflask/wqflask/static/new/javascript/dataset_select_menu.js wqflask/wqflask/templates/corr_scatter_plot_old.html | Lei Yan |
| 2014-06-25 | Added Karl's correlation matrix code...Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait | Zachary Sloan |
| 2014-05-05 | Committing a bunch of changes related to integrating GEMMA and...adding the correlation matrix page | Zachary Sloan |
| 2014-03-05 | Improved load_genotypes.py...Committer: Lei Yan <lei@penguin.uthsc.edu> On branch master | Lei Yan |
| 2014-02-28 | Made some changes to Lei's IO code for GN1 and GN2 genofiles | Lei Yan |
| 2014-02-23 | On branch master | Lei Yan |
| 2014-02-23 | On branch master | Lei Yan |
| 2014-02-23 | On branch master | Lei Yan |
| 2014-02-22 | On branch master | Lei Yan |
| 2014-02-22 | On branch master | Lei Yan |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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