| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2015-07-09 | Mapping methods now check for existing genotype files. | zsloan | |
| 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 | |||
| 2015-07-09 | Some phenotype searches were throwing an error due to an assert statement in ↵ | zsloan | |
| trait.py. Since I couldn't find the purpose of the assert statement I removed it. | |||
| 2015-07-07 | Updated mirror/development sites and changed font color in form control emements | zsloan | |
| 2015-07-07 | Also added index column to collections | zsloan | |
| 2015-07-07 | Added index column and changed the way location is displayed for search results | zsloan | |
| 2015-07-06 | Forgot to add the search error page template | zsloan | |
| 2015-07-06 | An error page should be loaded if the user uses a nonexistent search term, ↵ | zsloan | |
| instead of getting an Internal Server Error | |||
| 2015-07-02 | Merge branch 'master' of github.com:genenetwork/genenetwork2 | zsloan | |
| 2015-07-02 | Merge pull request #81 from lomereiter/fix_exporting | zsloan | |
| Fix SVG/PDF exporting | |||
| 2015-07-02 | Combined searches that didn't work previously should work now, including cis ↵ | zsloan | |
| and trans combined searches | |||
| 2015-07-02 | fix typos | Artem Tarasov | |
| 2015-07-02 | fix #80 | Artem Tarasov | |
| 2015-07-02 | use button for returning to full view | Artem Tarasov | |
| 2015-07-02 | added CairoSVG to misc/requirements | Artem Tarasov | |
| 2015-07-01 | Needed to add a couple parenthesis for transLRS searches | zsloan | |
| 2015-07-01 | Merge branch 'master' of github.com:genenetwork/genenetwork2 | zsloan | |
| 2015-07-01 | cis and trans LRS searches now work. Still need to get them working in ↵ | zsloan | |
| combined searches | |||
| 2015-06-29 | Merge pull request #72 from lomereiter/issue69 | zsloan | |
| Fixes #69 | |||
| 2015-06-29 | Merge pull request #77 from lomereiter/fix_sql | zsloan | |
| SQL security fixes | |||
| 2015-06-26 | Fixed minor bug where the static loading bar would remain after the mapping ↵ | zsloan | |
| results were displayed. | |||
| 2015-06-26 | Merge branch 'master' of github.com:genenetwork/genenetwork2 | zsloan | |
| 2015-06-26 | Fixed bug where mapping results sometimes wouldn't display. This would occur | zsloan | |
| due to a chromosome (in this case the last) not having any markers. Improved the way plink gets its path/command to use a method similar to the one Pjotr used with pylmm. I'll also do this for the other mapping methods. Fixed issue where the Y axis would always say LOD score. It now says LRS for mapping methods that return LRS Switched interval mapping (qtl reaper) to use the marker_regression template and removed the interval_mapping template (since it's unnecessary) Some commented out changes remain (in show_trait_mapping_tools and create_lodchart) from when I was attempting to open the mapping results in a new page. I had resolved every issue but the mapping javascript (lod_chart) not being able to access js_data (which has all the result data; markers, p-values, etc). I'm pretty sure that this is because js_data was inserted into the html after the page was loaded while the chart code ran immediately. I experimented with adding a short timeout to the mapping javascript and data table javascript, but while it worked for the table it did not work for the mapping figure. I don't know why this is. | |||
| 2015-06-26 | Added license file | pjotrp | |
| 2015-06-22 | Merge branch 'master' of github.com:genenetwork/genenetwork2 | zsloan | |
| Conflicts: wqflask/wqflask/templates/marker_regression.html | |||
| 2015-06-22 | Just a few minor changes before pulling Artem's fix to the mapping issue. | zsloan | |
| 2015-06-22 | Merge pull request #75 from lomereiter/fix_search | zsloan | |
| fix genotype search | |||
| 2015-06-22 | Merge pull request #76 from lomereiter/fix_mapping_results | zsloan | |
| fix mapping results loading | |||
| 2015-06-22 | escape docs query | Artem Tarasov | |
| 2015-06-22 | fixed a few potential security issues | Artem Tarasov | |
| 2015-06-21 | fix mapping results loading | Artem Tarasov | |
| 2015-06-20 | fix genotype search | Artem Tarasov | |
| 2015-06-18 | Fixed issue that prevented multiple mapping submissions without refreshing. ↵ | zsloan | |
| Also changed to where results open in new window instead of colorbox, though an issue remains where the css doesn't seem to be getting imported properly. | |||
| 2015-06-18 | removed unused function | Artem Tarasov | |
| 2015-06-18 | fix all_samples_ordered | Artem Tarasov | |
| move duplicated code into a method, handle the case of missing f1/f12 correctly | |||
| 2015-06-18 | add missing line to webqtlUtil | Artem Tarasov | |
| 2015-06-17 | Now you can expand/contract tabs on the trait page by click anywhere on the bar | zsloan | |
| 2015-06-16 | Finished adding all the extra tools/links below the trait details | zsloan | |
| 2015-06-05 | Added back in some of the options on the trait page; Add, Find, and Verify ↵ | zsloan | |
| now work. I'll get the other 4 working next. | |||
| 2015-06-04 | Fixed a minor issue that was causing position search to not work. | zsloan | |
| 2015-06-02 | Wildcards can now be appended to mRNA assay searches, but isn't working ↵ | zsloan | |
| correctly yet with phenotypes | |||
| 2015-06-02 | Added Panduka's Genotation tool link to the trait page, along with the Gene, ↵ | zsloan | |
| OMIM, and GenBank links | |||
| 2015-06-02 | Wildcard search should now work for Genotype searches | zsloan | |
| 2015-06-02 | Wildcard search (*) works for regular mRNA assay and phenotype searches and ↵ | zsloan | |
| fixed issue with black columns in correlation page | |||
| 2015-05-26 | Merge pull request #60 from lomereiter/pp | zsloan | |
| add missing file | |||
| 2015-05-26 | add missing file | Artem Tarasov | |
| 2015-05-26 | Merge pull request #58 from lomereiter/pp | zsloan | |
| Use NVD3 for bar chart and probability plot | |||
| 2015-05-26 | fix terminology | Artem Tarasov | |
| 2015-05-26 | use NVD3 for bar charts | Artem Tarasov | |
| added informative tooltips and error bars | |||
| 2015-05-23 | pp group selection | Artem Tarasov | |
| 2015-05-23 | fix group selection in blocking by index | Artem Tarasov | |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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