| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2013-01-23 | Added a bunch to notes and created new notes file specifically | Zachary Sloan | |
| related to installing a new instance of GN | |||
| 2013-01-22 | Added a couple things to notes regarding installing mysql client | Zachary Sloan | |
| 2013-01-22 | Pushed through a few errors in getting the correlation page running | 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 | |||
| 2013-01-11 | Commented out import of rpy2 in correlationFunction.py due to | Zachary Sloan | |
| problem with rpy2 | |||
| 2013-01-11 | Upgraded packages requirements.txt but haven't tested | Zachary Sloan | |
| 2013-01-11 | Overwrote requirements.txt | Zachary Sloan | |
| 2013-01-11 | Trimmed a bunch of code off of marker_regression.py | Zachary Sloan | |
| 2013-01-10 | Checking in before we try to write our own code for the manhattan | Zachary Sloan | |
| plot figure` | |||
| 2013-01-10 | Checking in before trying to put manhattan plot sections closer together | Zachary Sloan | |
| 2013-01-10 | Normalized the y axis for each manhattan plot section | Zachary Sloan | |
| 2013-01-10 | The plots now correctly appear above/below each other. | Zachary Sloan | |
| Committing before trying to combine all the manhattan plot segments | |||
| 2013-01-10 | Edited marker_regression.coffee to make every sub-manhattan plot | Zachary Sloan | |
| for each chromosome display Created css file for the marker_regression page Currently has display issue where the permutation histogram is overlapping with the manhattan plot | |||
| 2013-01-10 | Made Chromosome class in marker_regression.coffee; current | Zachary Sloan | |
| it writes each chromosome's manhattan plot on top of each other. This commit is before trying to fix that. | |||
| 2013-01-10 | Made x-axis values into ints; committing before trying to add multiple graphs | Zachary Sloan | |
| for each chromosome | |||
| 2013-01-10 | Worked with the manhattan plot coffeescript to set x-axis and change | Zachary Sloan | |
| the plot point sizes and remove lines | |||
| 2013-01-09 | Manhattan plot results are appearing correctly for chromosome 1 | Zachary Sloan | |
| 2013-01-09 | The histogram coffeescript is now in its own class and the graph | Zachary Sloan | |
| still displays correctly | |||
| 2013-01-09 | Checking in before putting the histogram coffeescript into its own | Zachary Sloan | |
| class | |||
| 2013-01-09 | More or less finished the permutation histogram | Zachary Sloan | |
| 2013-01-09 | Got the permutation plot working as a line plot; still need to make | Zachary Sloan | |
| it into a bar graph, though | |||
| 2013-01-09 | jqplot added | Zachary Sloan | |
| 2013-01-09 | Got the marker regression page to display again | Zachary Sloan | |
| Passed lrs_array values as js_data for the permutation histogram | |||
| 2013-01-08 | js_data is being printed out (seemingly) correctly now for the | Zachary Sloan | |
| marker_regression page | |||
| 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 | |||
| 2013-01-04 | Continued rewriting marker_regression.py code | Zachary Sloan | |
| 2013-01-04 | Correct results are being returned from reaper for the marker regression page | Zachary Sloan | |
| 2013-01-03 | Began working on marker_regression.py and created Chromosomes class | Zachary Sloan | |
| in species.py | |||
| 2013-01-03 | marker_regression page is up again | Zachary Sloan | |
| 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 | |||
| 2012-12-20 | Changed layout of marker regression options | Zachary Sloan | |
| 2012-12-20 | The control locus field in the interval mapping settings is now disabled if | Zachary Sloan | |
| "choose closest control" is set to "yes" | |||
| 2012-12-20 | Made composite mapping options show/hide for the interval mapping section | Zachary Sloan | |
| 2012-12-20 | More changes to the layout of interval mapping options | Zachary Sloan | |
| 2012-12-20 | Continued to customize the interval mapping menu | Zachary Sloan | |
| 2012-12-20 | Improved appearance/layout of the interval mapping tab using bootstrap | Zachary Sloan | |
| 2012-12-20 | Form data passed via POST for marker regression | Zachary Sloan | |
| Removed "Use Parents" and "Use Weighted" Created text box to input # permutations for pair scan | |||
| 2012-12-18 | Changed html for the marker regression tab | Zachary Sloan | |
| Created file show_trait_mapping_tools.coffee to handle submitting the form to the marker regression page Changed form name/id in show_trait.html to "trait_data_form" | |||
| 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 links working for statistics table labels | Zachary Sloan | |
| 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 | |||
| 2012-12-07 | Got show_trait page to appear again for phenotype traits | Zachary Sloan | |
| Need to see why other samples list doesn't appear for traits in BXDPublishedPhenotypes | |||
| 2012-12-06 | All 10 stats working | Zachary Sloan | |
| 2012-12-06 | Continued work on basic statistics table in show_trait | Zachary Sloan | |
| Continued work towards getting show_trait to work with phenotype 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 | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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