genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2013-04-02	pylmm code is running for human data (plink .bed genotype files)	Zachary Sloan

2013-03-28	quick_search_table.py seems to be running OK for the PublishXRef	Zachary Sloan
	table, but will need to check later to make sure
2013-03-26	Just checking in code while in the process of trying to get	Zachary Sloan
	the quick search working properly
2013-03-22	Removed zach_settings.py from git tracking	Zachary Sloan
	Changed mysql password as a result of it being up on git before
2013-03-21	Did some work towards getting Nick's code working with our plink	Zachary Sloan
	human genotype files Tried to get the automatic searches working when points are highlighted on the marker regression manhattan plot
2013-03-19	In the process of trying to use Nick's pylmmKinship.py code to	Zachary Sloan
	precompute the kinship matrix for the human datasets we have plink .bed genotype data for
2013-03-19	Added Nick's input.py file which uses plink .ped files as input	Zachary Sloan
	for his pylmm code
2013-03-08	Caching is working for marker regression but really slowly	Zachary Sloan

2013-03-08	Refactored GWAS function in lmm.py	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
2013-03-07	Created file temp_data to store data related to progress	Zachary Sloan
	of the marker regression calculations Storing progress of kinship matrix calculation in variable as portion of 45 (the rough percent of total marker regression calculation time
2013-03-06	Stored percent of calculate_kinship function completion in	Zachary Sloan
	variable
2013-02-28	Added benchmark.py that compares the time of various operations	Zachary Sloan
	and gives a report with the percent of total computation time each takes
2013-02-21	Add my_pylmm package	Zachary Sloan

2013-02-13	Got results displaying for BXD and fixed genofile_parser.py to work	Zachary Sloan
	for all of our genofiles
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
2013-02-08	Converted .geno files to json files and wrote code in marker_regression.py	Zachary Sloan
	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)
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
2013-02-06	Edited genofile_parser.py to go through all genofiles and convert	Zachary Sloan
	them to the format used by nick's code