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2013-02-13Fixed some bugs related to getting the marker regression page working...with Nick's code Zachary Sloan
2013-02-12Edited marker_regression.py and data_set.py to store the p-values...and their corresponding markers to be used in the table of qtl results and other figures Zachary Sloan
2013-02-08Converted .geno files to json files and wrote code in marker_regression.py...that loads the json files, converts them into the relevant numpy arrays, and passes them into Nick's code (which is returning results that may or may not be correct, but is at least running) Zachary Sloan
2013-02-07Added code to marker_regression.py that creates the numpy arrays to...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 Zachary Sloan
2013-02-06Edited genofile_parser.py to go through all genofiles and convert...them to the format used by nick's code Zachary Sloan
2013-02-06Added changes to example.py and prep_data.py that lets nick's code read in...our data Zachary Sloan
2013-02-06Small change to search_results.py to get search results page to workZachary Sloan
2013-01-31Added wqflask-nginx.confZachary Sloan
2013-01-31Copied over nginx.conf from /etc/nginxZachary Sloan
2013-01-31Merge branch 'flask' of http://github.com/zsloan/genenetwork into flaskZachary Sloan
2013-01-31Deleted nginx.conf from the other_conf directory not in wqflaskZachary Sloan
2013-01-31Merge branch 'flask' of https://github.com/zsloan/genenetwork into flaskZachary Sloan
2013-01-31Changed reference to 'dataset_name' in keywords to 'dataset' to get...page to work, but will change all references to the dataset name to 'dataset_name' in future to avoid confusion between the dataset name and the actual dataset object Zachary Sloan
2013-01-31Changed fd to kw in search_results.py, commented out some lines...related to fd Zachary Sloan
2013-01-25Added a bunch of things to notesZachary Sloan
2013-01-25Merge branch 'flask' of http://github.com/zsloan/genenetwork into flaskZachary Sloan
2013-01-25Fixed a few bugs while trying to get the code running on the new serverZachary Sloan
2013-01-24Added a lot to the notes in the process of setting up on the...new server Zachary Sloan
2013-01-23Added a bunch to notes and created new notes file specifically...related to installing a new instance of GN Zachary Sloan
2013-01-22Added a couple things to notes regarding installing mysql clientZachary Sloan
2013-01-22Pushed through a few errors in getting the correlation page runningZachary Sloan
2013-01-18Renamed CorrelationPage.py to show_corr_results.py...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 Zachary Sloan
2013-01-11Commented out import of rpy2 in correlationFunction.py due to...problem with rpy2 Zachary Sloan
2013-01-11Upgraded packages requirements.txt but haven't testedZachary Sloan
2013-01-11Overwrote requirements.txtZachary Sloan
2013-01-11Trimmed a bunch of code off of marker_regression.pyZachary Sloan
2013-01-10Checking in before we try to write our own code for the manhattan...plot figure` Zachary Sloan
2013-01-10Checking in before trying to put manhattan plot sections closer togetherZachary Sloan
2013-01-10Normalized the y axis for each manhattan plot sectionZachary Sloan
2013-01-10The plots now correctly appear above/below each other....Committing before trying to combine all the manhattan plot segments Zachary Sloan
2013-01-10Edited marker_regression.coffee to make every sub-manhattan plot...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 Zachary Sloan
2013-01-10Made Chromosome class in marker_regression.coffee; current...it writes each chromosome's manhattan plot on top of each other. This commit is before trying to fix that. Zachary Sloan
2013-01-10Made x-axis values into ints; committing before trying to add multiple graphs...for each chromosome Zachary Sloan
2013-01-10Worked with the manhattan plot coffeescript to set x-axis and change...the plot point sizes and remove lines Zachary Sloan
2013-01-09Manhattan plot results are appearing correctly for chromosome 1Zachary Sloan
2013-01-09The histogram coffeescript is now in its own class and the graph...still displays correctly Zachary Sloan
2013-01-09Checking in before putting the histogram coffeescript into its own...class Zachary Sloan
2013-01-09More or less finished the permutation histogramZachary Sloan
2013-01-09Got the permutation plot working as a line plot; still need to make...it into a bar graph, though Zachary Sloan
2013-01-09jqplot addedZachary Sloan
2013-01-09Got the marker regression page to display again...Passed lrs_array values as js_data for the permutation histogram Zachary Sloan
2013-01-08js_data is being printed out (seemingly) correctly now for the...marker_regression page Zachary Sloan
2013-01-08Created IndChromosome class in species.py and wrote functions for...chromosome-related attributes Began to try and pass qtlreaper results as js_data to use when drawing graphs Zachary Sloan
2013-01-08Deleted some unnecessary code in marker_regression.py and fixed some bugs...Added a couple utility functions to the Chromosomes class in species.py Zachary Sloan
2013-01-04Continued rewriting marker_regression.py codeZachary Sloan
2013-01-04Correct results are being returned from reaper for the marker regression pageZachary Sloan
2013-01-03Began working on marker_regression.py and created Chromosomes class...in species.py Zachary Sloan
2013-01-03marker_regression page is up againZachary Sloan
2013-01-03Created template for marek regression page and made the compute button direct...to it added asbolute_import in data_set.py and trait.py Made several minor changes and deleted commented out code in trait.py Zachary Sloan
2012-12-20Changed layout of marker regression optionsZachary Sloan
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