| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2015-07-09 | Some phenotype searches were throwing an error due to an assert statement in ... | zsloan |
| 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, in... | zsloan |
| 2015-07-02 | Merge branch 'master' of github.com:genenetwork/genenetwork2 | zsloan |
| 2015-07-02 | Combined searches that didn't work previously should work now, including cis ... | zsloan |
| 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 |
| 2015-07-01 | 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 combin... | zsloan |
| 2015-06-29 | Merge pull request #72 from lomereiter/issue69...Fixes #69 | zsloan |
| 2015-06-29 | Merge pull request #77 from lomereiter/fix_sql...SQL security fixes | zsloan |
| 2015-06-26 | Fixed minor bug where the static loading bar would remain after the mapping r... | zsloan |
| 2015-06-26 | Fixed bug where mapping results sometimes wouldn't display. This would occur...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.
| zsloan |
| 2015-06-22 | Merge branch 'master' of github.com:genenetwork/genenetwork2...Conflicts:
wqflask/wqflask/templates/marker_regression.html
| zsloan |
| 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...fix genotype search | zsloan |
| 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. A... | zsloan |
| 2015-06-18 | removed unused function | Artem Tarasov |
| 2015-06-18 | fix all_samples_ordered...move duplicated code into a method,
handle the case of missing f1/f12 correctly
| Artem Tarasov |
| 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 no... | zsloan |
| 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 corre... | zsloan |
| 2015-06-02 | Added Panduka's Genotation tool link to the trait page, along with the Gene, ... | zsloan |
| 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 f... | zsloan |
| 2015-05-26 | Merge pull request #60 from lomereiter/pp...add missing file | zsloan |
| 2015-05-26 | add missing file | Artem Tarasov |
| 2015-05-26 | Merge pull request #58 from lomereiter/pp...Use NVD3 for bar chart and probability plot | zsloan |
| 2015-05-26 | fix terminology | Artem Tarasov |
| 2015-05-26 | use NVD3 for bar charts...added informative tooltips and error bars
| Artem Tarasov |
| 2015-05-23 | pp group selection | Artem Tarasov |
| 2015-05-23 | fix group selection in blocking by index | Artem Tarasov |
| 2015-05-23 | Fix trait grouping | Artem Tarasov |
| 2015-05-23 | new probability plot (using NVD3 library)...* z scores are computed on the client side (using jStat library)
* added Shapiro-Wilk test results
| Artem Tarasov |
| 2015-05-22 | Fixed issue where correlation didn't work for human traits (and probably some... | zsloan |
| 2015-05-21 | Changed the digits for additive effect and megabases in the search results table | zsloan |
| 2015-05-20 | Merge pull request #53 from lomereiter/bar_chart_improvements...Bar chart improvements | zsloan |
