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2015-10-12Changed the location filter for correlation pagezsloan
2015-09-11Comment out some excessive stdout spamDannyArends
2015-09-10Fixed "TypeError: float argument required, not NoneType" about mean.Lei Yan
Committer: Lei Yan <lei@penguin.uthsc.edu> On branch master
2015-08-26Fixed issue with colums for the gene global search (still need to change for ↵zsloan
phenotype) Fixed issue where LRS and LOD are sometimes labeled incorrectly Changed the header of the trait page Added link to GN1 in header Fixxed an issue that made permutations not work with pylmm Fixed "sign in" button when creating a collection while not logged in
2015-07-20Fixed the code that generates the dataset selection drop-down for correlationszsloan
Made changes to the tables of correlation results, collections, and search results: - Added resizeable columns to correlation results and collections, but not to search results because it seems that it requires Y scrolling to be set (I'll check if it makes sense to add scrolling to the search results) - Correlation results and collections are now in scrolling tables - The style is the same across all of these tables now Remaining issues: - It doesn't seem like I can set the column width when initializing dataTables in correlation results. I don't know why this is; it might be due to the table already being the size of a full page. I want to be able to default to some good widths, even if the user can resize them - I tried adding hoverForMore, but it doesn't seem to cooperate with datatable cells; I think this is due to having to put the text in a div.
2015-07-10Fixed the genofile_parser.py script since some .geno files had been ↵zsloan
incorrectly converted to json Fixed GO search to work with combined searches
2015-07-09Mapping 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
2015-07-09Some 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.
2015-07-07Added index column and changed the way location is displayed for search resultszsloan
2015-06-29Merge pull request #72 from lomereiter/issue69zsloan
Fixes #69
2015-06-22fixed a few potential security issuesArtem Tarasov
2015-06-18fix all_samples_orderedArtem Tarasov
move duplicated code into a method, handle the case of missing f1/f12 correctly
2015-05-26Merge pull request #58 from lomereiter/ppzsloan
Use NVD3 for bar chart and probability plot
2015-05-23new probability plot (using NVD3 library)Artem Tarasov
* z scores are computed on the client side (using jStat library) * added Shapiro-Wilk test results
2015-05-22Fixed issue where correlation didn't work for human traits (and probably ↵zsloan
some others)
2015-05-21Changed the digits for additive effect and megabases in the search results tablezsloan
2015-05-13combine three similar queries into oneArtem Tarasov
2015-05-13replace multiple tissue queries with a single oneArtem Tarasov
2015-05-13cache datasets for each groupArtem Tarasov
2015-05-12Resolved conflict before commitzsloan
2015-05-12Fix #35Artem Tarasov
* 'aliases' and 'location' are shown only where relevant * descriptions for phenotype datasets are provided at the top
2015-05-11Moved chunksPjotr Prins
2015-05-11Moving pylmm out of the treepjotrp
2015-04-10Added git large file system (the .gitattributes files) and fixed an issue ↵zsloan
where rat trait pages wouldn't work
2015-03-27Changed HTMLPATH in webqtlConfig since I forgot to in the last commit (since ↵zsloan
it used to point to the now-renamed 'web' directory). It obviously also needs to be renamed later, but I'll have to find every place that calls webqtlConfig.HTMLPATH first to do so.
2015-03-26Removed several unused files from the base folder and their references in ↵zsloan
other files
2015-03-25Pair scan image now loads properlyzsloan
2015-03-24Change back port location and home directory location; this should be in ↵zsloan
external settings
2015-03-23Updates to make GN2 work on my version of penguin (ports, and paths)DannyArends
2015-03-17Converting an absolute path to a relative pathDannyArends
2015-01-30Fixed several bugsZachary Sloan
Added legend to bar chart color by trait function Added scatterplot matrix figure Fixed database timeout problem
2014-12-12Added a additive effect column to search result and collection tablesZachary Sloan
Fixed the header so that it looks fine when resizing
2014-11-17Just more changes converting to bootstrap 3Zachary Sloan
2014-10-17Added reference, policies, and links pagesZachary Sloan
Improved the appearance of the header menu and "title bar"
2014-10-02Fixed an error when there's no locus for mRNA expression traitsZachary Sloan
2014-08-21Committer: Lei Yan <lei@penguin.uthsc.edu>Lei Yan
On branch master
2014-08-21Added the option to display mapping results as either an interval mappingZachary Sloan
or manhattan plot Fixed a few minor bugs
2014-07-21Fixed issue where sample values were ordered on the trait pageZachary Sloan
2014-07-18Merge /home/zas1024/geneLei Yan
Conflicts: wqflask/base/data_set.py
2014-07-18Added outlier highlightingZachary Sloan
Changed order of tabs in statistics panel on trait page Started working on heatmap
2014-07-18Correlation table for phenotypes is workingLei Yan
2014-07-09Updated coffeescript, svg export working fine, interval mapping zoom workingZachary Sloan
2014-06-25Added Karl's correlation matrix codeZachary Sloan
Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait
2014-06-06Implimented Karl Broman's lodchart code for the interval mapping function.Zachary Sloan
Suggestive/significant bars and additive effect curve added
2014-05-05Committing a bunch of changes related to integrating GEMMA andZachary Sloan
adding the correlation matrix page
2014-02-28Committing after creating AnonCollection class and before addingZachary Sloan
remove trait function
2014-02-28Made some changes/comments to Lei's load_genotypes.py fileZachary Sloan
2014-02-27Began working on a TraitCollection.py file that will contain both theZachary Sloan
object for logged in user collections and collections created by anonymous users.
2014-01-30Most of the work is done towards running lmm.py from the command lineZachary Sloan
and storing the results in redis
2014-01-29Limited number of markers in marker regression result table toZachary Sloan
those with a lod score > 2 Did some work towards adding the colored backgrounds to chromosome areas in the manhattan plot Changed the last two chromosomes for human manhattan plots to X and X/Y Started work on writing a script that can independently run the pyLMM code and store the results in redis