| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2013-03-12 | Added the script generating probesetfreeze data matrix files | Zachary Sloan | |
| The script was created to regenerate a bad file for Evan | |||
| 2013-03-12 | Got cashing working with pickle | Zachary Sloan | |
| 2013-03-07 | Progress bar is now completely working | Zachary Sloan | |
| Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code | |||
| 2013-03-02 | Created generate_probesetfreeze_file to create the | Zachary Sloan | |
| "probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with | |||
| 2013-02-22 | Added some to notes | Zachary Sloan | |
| 2013-02-14 | Have marker regression results displaying as a scatterplot (just the points) | Zachary Sloan | |
| using d3.js | |||
| 2013-02-13 | Fixed some bugs related to getting the marker regression page working | Zachary Sloan | |
| with Nick's code | |||
| 2013-02-12 | Edited marker_regression.py and data_set.py to store the p-values | Zachary Sloan | |
| and their corresponding markers to be used in the table of qtl results and other figures | |||
| 2013-02-07 | Added code to marker_regression.py that creates the numpy arrays to | Zachary Sloan | |
| pass to Nick's code and changed the prep_data.py code to operate on a list of phenotype values instead of a textfile with the values delimited | |||
| 2013-01-31 | Changed fd to kw in search_results.py, commented out some lines | Zachary Sloan | |
| related to fd | |||
| 2013-01-25 | Fixed a few bugs while trying to get the code running on the new server | Zachary Sloan | |
| 2013-01-18 | Renamed CorrelationPage.py to show_corr_results.py | Zachary Sloan | |
| Worked with correlation code; got to the code that begins to do the actual correlations Created a function "get_dataset_and_trait" in the new file "helper_functions.py" because the code initializing the dataset and trait objects was repeated in multiple places | |||
| 2013-01-08 | Created IndChromosome class in species.py and wrote functions for | Zachary Sloan | |
| chromosome-related attributes Began to try and pass qtlreaper results as js_data to use when drawing graphs | |||
| 2013-01-08 | Deleted some unnecessary code in marker_regression.py and fixed some bugs | Zachary Sloan | |
| Added a couple utility functions to the Chromosomes class in species.py | |||
| 2013-01-03 | Began working on marker_regression.py and created Chromosomes class | Zachary Sloan | |
| in species.py | |||
| 2013-01-03 | Created template for marek regression page and made the compute button direct | Zachary Sloan | |
| to it added asbolute_import in data_set.py and trait.py Made several minor changes and deleted commented out code in trait.py | |||
| 2012-12-18 | Created new file species.py and species class object TheSpecies | Zachary Sloan | |
| Converted html for the mapping tabs to bootstrap and redid html inside of the Interval Mapping tab Added text input for # of permutation tests and bootstrap tests | |||
| 2012-12-07 | Got basic statistics in show_trait to display the correct number | Zachary Sloan | |
| of samples for each group Got show_trait page to display for genotype traits | |||
| 2012-12-06 | Added minimum/maximum to basic statistics table | Zachary Sloan | |
| Continued bug-shooting related to getting show_trait running with phenotype traits | |||
| 2012-12-06 | Got show_trait running again for MrnaAssay traits | Zachary Sloan | |
| 2012-12-06 | Made many small changes to show_trait/data_set/search_results/trait to | Zachary Sloan | |
| remove use of the formData object and cursor | |||
| 2012-12-05 | Renamed webqtlTrait.py to trait.py | Zachary Sloan | |
| Renamed webqtlTrait class to GeneralTrait Began process of removing fd from show_trait.py Created DatasetGroup object in data_set.py (this may end up becoming its own file later if it becomes big enough) | |||
| 2012-12-05 | Continued to make changes related to getting rid of cursor/db_conn | Zachary Sloan | |
| and using simple sqlalchemy Got Pheno/MrnaAssay dataset searches working again | |||
| 2012-12-04 | Changed parser to allow quotes (i.e. name="rw williams") | Zachary Sloan | |
| Renamed webqtlTrait to GeneralTrait and began rewriting parts Changed database code in many places to use simple sqlalchemy | |||
| 2012-12-04 | Began changing references to cursor/db_conn to use sqlalchemy | Zachary Sloan | |
| Wrote function for phenotype author searches | |||
| 2012-11-30 | Added example of escaping strings now that trasitioning to simple SQLAlchemy | Zachary Sloan | |
| 2012-11-30 | Started switching to using basic sqlalchemy to handle db connection/queries | Zachary Sloan | |
| Began fixing bugs related to this fix, still in progress | |||
| 2012-11-29 | Changed a number of variables (riset to group, db to dataset) | Zachary Sloan | |
| Put most of the code for cisLRS and transLRS searches into the class CisTransLrsSearch (might change this name to something else later) Simplified escape code for searches in do_search.py Got search_results working again after some changes | |||
| 2012-11-28 | Made some small changes to get code working for genotype searches | Zachary Sloan | |
| 2012-11-27 | Created subclass for each main data set type and moved the code | Zachary Sloan | |
| for getting trait info that was in search_results.py into its respective class Renamed webqtlDataset to DataSet/create_dataset in webqtlTrait.py, webqtlDatabaseFunction.py, and CorrelationPage.py Got search page running again for mRNA assay data sets with these changes | |||
| 2012-11-27 | Renamed webqtlDataSet.py to data_set.py | Zachary Sloan | |
| Renamed the class webqtlDataset to DataSet Finished cisLRS and transLRS search types in d_search.py Fixed parent/f1 issue in show_trait.py | |||
| 2012-10-30 | Worked on search_result.py code related to adding clause item to queries | Zachary Sloan | |
| Continued work on redesigning the trait data page design | |||
| 2012-10-26 | Got search page working for mice with a single gene search | Zachary Sloan | |
| 2012-10-25 | Worked on search page code; got to the part that actually does the search | Zachary Sloan | |
| Renamed RISet and cross to "group" throughout webqtlDataset.py and search_results.py | |||
| 2012-10-24 | Now builds json datastructure for menus correctly | Zachary Sloan | |
| 2012-10-23 | Finished coffeescript that handles the home page dataset selection dropdowns | Zachary Sloan | |
| 2012-09-28 | Removed show_trait_page.py and moved relevant code over to ↵ | Zachary Sloan | |
| DataEditingPage.py (though the user security stuff still needs to be moved over) | |||
| 2012-09-28 | Finished getting extra attributes to display correctly in the trait data table | Zachary Sloan | |
| 2012-09-27 | Worked on getting attributes in the SampleList object to display data ↵ | Zachary Sloan | |
| properly, changed SampleList from an object list to object | |||
| 2012-09-25 | Got trait data page running for human dataset, changed list of sample ↵ | Zachary Sloan | |
| objects to a SampleList object | |||
| 2012-09-25 | Fixed issue with parent strains appearing twice and began replacing variable ↵ | Zachary Sloan | |
| names (strain -> sample, for example) | |||
| 2012-09-19 | Made pearson/spearman options disappear if lit correlation is chosen, began ↵ | Zachary Sloan | |
| to address how to deal with Trait object in CorrelationPage | |||
| 2012-09-14 | Got the dynamic javascript stats table working | Zachary Sloan | |
| 2012-09-13 | Worked on improving readData and informativeStrains functions in ↵ | Zachary Sloan | |
| webqtlFormData while trying to get correlation page running | |||
| 2012-09-12 | Worked towards correctly passing form data to correlation page and addressed ↵ | Zachary Sloan | |
| various bugs that arose while doing so | |||
| 2012-09-07 | Worked with passing form data to correlation page | Zachary Sloan | |
| 2012-08-29 | Fixed so that outliers are now correctly highlighted | Zachary Sloan | |
| 2012-08-28 | Various changes related to the webqtlCaseData object and the way ↵ | Zachary Sloan | |
| values/variances/num_cases are called in DataEditingPage.py | |||
| 2012-08-23 | Various minor changes | Zachary Sloan | |
| 2012-06-06 | Most of the top fields working | Sam Ockman | |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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