| Age | Commit message (Expand) | Author |
|---|
| 2019-01-17 | Redid gene global search to take JSON data input instead of converting an HTM......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
| zsloan |
| 2019-01-16 | Pushing SNP browser updates | zsloan |
| 2019-01-11 | Got InDel working for Variant Browser...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
| zsloan |
| 2018-12-21 | Fixed collections so they can be very large (1000+ traits)...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
| zsloan |
| 2018-12-05 | Fixed Verify link | zsloan |
| 2018-12-05 | Fixed issue where SNP track for mapping did not appear correctly...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
| zsloan |
| 2018-11-20 | Added option to select chromosome from trait page when mapping...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
| zsloan |
| 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 inconsi......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)
:
| zsloan |
| 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 |
| 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 | - 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 |
| 2018-10-12 | Fixed issue that caused error when mapping single-chromosome, since a second ... | zsloan |
| 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 |
| 2018-09-15 | 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...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 |
| 2018-07-06 | 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 branch 'testing' of https://github.com/fredmanglis/genenetwork2 into te... | Pjotr Prins |
| 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 |
| 2018-04-16 | Docs on elasticsearch use | Pjotr Prins |
| 2018-04-15 | Deactivate analysis of email_address field...* Prevent elasticsearch from analysing and tokenising the email_address
field so as to avoid issue with getting back all email addresses with
the same domain as the one being searched for.
| Muriithi Frederick Muriuki |
