| Age | Commit message (Expand) | Author |
|---|
| 2018-11-04 | Quick fix to issue where GEMMA wouldn't be run simultaneously on traits from ... | zsloan |
| 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 using... | zsloan |
| 2018-11-01 | Updated the way snpbrowser initializes parameters, in preparation for drawing......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
| zsloan |
| 2018-10-24 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
| 2018-10-24 | - SNP Browser is mostly complete; just need to test more and add SNP density ......- 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"
| zsloan |
| 2018-10-15 | Added "as root" for instructions on running ES...Forgot to add to change user to root during the last commit | zsloan |
| 2018-10-15 | Updated instructions for running elasticsearch...Since I know I'll forget otherwise, updated instructions on starting up ES | zsloan |
| 2018-10-12 | Fixed issue that caused error when mapping single-chromosome, since a second ... | zsloan |
| 2018-10-12 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into gn-testing | Pjotr Prins |
| 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 | 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 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 |
| 2018-09-17 | Merge pull request #342 from pjotrp/gemma-20180915...Gemma optimized for production | zsloan |
| 2018-09-15 | Run gemma without debug and checks in production | Pjotr Prins |
| 2018-09-15 | ES comment | Pjotr Prins |
| 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 |
| 2018-08-23 | Added "change user to elasticsearch"...Added "change user to elasticsearch" to the description of how to start elasticsearch | zsloan |
| 2018-08-15 | The issue with adding anonymous collections should be fixed now | zsloan |
| 2018-08-15 | ES comment | Pjotr Prins |
| 2018-08-14 | Fixed minor issue in user_manager.py | zsloan |
| 2018-08-14 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan |
| 2018-08-14 | Added cofactors to correlation scatterplot and changed it to use Plotly...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
| zsloan |
| 2018-08-10 | Added the command needed to start up elasticsearch...I added the command to start elasticsearch, since I've had to look it up/ask Pjotr about it a couple times now. | zsloan |
| 2018-07-06 | Added square root transform options...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
| zsloan |
| 2018-07-02 | Added option to transform/normalize trait sample values (log2 and qnorm) on t......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
| zsloan |
| 2018-06-08 | Added option to add traits to existing collection, which I had forgotten prev... | zsloan |
| 2018-06-08 | User collections (now stored in ElasticSearch) are reimplemented now and shou... | 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 |
| 2018-05-01 | Merge /home/lei/gene into testing | zsloan |
| 2018-05-01 | Removed all code related to using GEMMA with PLINK input files | zsloan |
| 2018-04-27 | Added marker filtering for data set groups with larger genotype files...Fixed issue where GEMMA + LOCO wasn't working with AIL (and probably some other groups)
| 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 |
| 2018-04-19 | Changed width of top bar and a couple other html objects to 100% instead of s......Changed to using BIMBAM files to build Marker objects in dataset.py
| zsloan |
| 2018-04-18 | Removed a little more code in webqtlDatabaseFunction.py and do_search | zsloan |
| 2018-04-16 | Undoing changes to user_manager.py, because I think they may have caused some... | zsloan |
| 2018-04-16 | Resolved conflicts after pulling changes | zsloan |
| 2018-04-16 | Removed some unused code from collect.py and user_manager.py | zsloan |
| 2018-04-16 | Removed file tracer.py that wasn't being used...Removed some unused code from the other files listed
| zsloan |
| 2018-04-16 | Removed a bunch of unused code from the following files:...marker_regression_gn1.py
marker_regression.py
do_search.py
export_traits.py
heatmap.py
GeneUtil.py
heatmap.html
| zsloan |
| 2018-04-16 | Merge pull request #318 from pjotrp/testing...Testing | zsloan |
| 2018-04-16 | Merge branch 'testing' of https://github.com/fredmanglis/genenetwork2 into te... | Pjotr Prins |
| 2018-04-16 | Merge pull request #317 from pjotrp/testing...Testing | zsloan |
| 2018-04-16 | Remove statements that might be causing issues...* I can't swear on this, but it seems the presence of these statements
was causing elasticsearch to act weird.
| Muriithi Frederick Muriuki |
| 2018-04-16 | login messages improved | Pjotr Prins |
| 2018-04-16 | Merge remote-tracking branch 'pjotrp/testing' into testing | Muriithi Frederick Muriuki |
| 2018-04-16 | Update mappings for Elasticsearch 6.2. Update logger...* Update the indexes mappings to be compatible with the newer
Elasticsearch 6.2.* series.
Close the index before updating it, and reopen it after to help with
the re-indexing of the data.
* Update the error logger to include the exception that was thrown.
| Muriithi Frederick Muriuki |
