genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2014-06-06	Implimented Karl Broman's lodchart code for the interval mapping function.	Zachary Sloan
	Suggestive/significant bars and additive effect curve added
2014-05-05	Committing a bunch of changes related to integrating GEMMA and	Zachary Sloan
	adding the correlation matrix page
2014-01-30	Most of the work is done towards running lmm.py from the command line	Zachary Sloan
	and storing the results in redis
2014-01-29	Limited number of markers in marker regression result table to	Zachary 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
2014-01-23	Histogram is working	Zachary Sloan
	Fixed some bug with generating the manhattan plot for the HLC data set
2014-01-03	Wrote some code for the histogram figure	Zachary Sloan
	Changed some code in dataset to try and track down the issue with Amelie's file
2013-11-26	Made some progress towards getting the traits inside a collection to display ↵	Zachary Sloan
	on hover
2013-11-25	Got the interval mapping results into a table	Zachary Sloan

2013-10-25	Began working on color coding bar chart by extra attributes	Zachary Sloan

2013-10-15	Changed templates to call the header macro	Zachary Sloan
	Correlation page now works with Non-BXD (or whatever group) or All Samples options
2013-10-11	Merge /home/lei/gene	Zachary Sloan
	Conflicts: wqflask/maintenance/quick_search_table.py
2013-10-10	Almost have correlation working for non-primary strain/group	Lei Yan
	There's just some issue with parents/f1s not being included if you select non-BXD (or whatever the group is). All Samples, however does work.
2013-10-09	Improved some of the code related to the correlation page	Lei Yan
	For example, changed the two functions getting gene symbols and ids for a dataset into one function that can take a column name as a parameter
2013-10-08	Literature correlation works when it is selected as the sorted	Lei Yan
	correlation type (that is, when it is run again all traits in a database) Added a function to data_set.py that gets all the gene_ids in the data set. Not sure if having a separate function for getting the gene_ids and another for getting the gene symbols makes sense.
2013-10-08	Did some work with interval mapping page; will use qtl reaper to do	Zachary Sloan
	the mapping, since it is reliable/fast and avoids us having to rewrite from scratch using something like r/qtl
2013-09-24	Did some work towards doing the tissue correlation for all traits	root
	in a dataset (in order to sort by tissue correlation instead of sample correlation).
2013-08-21	Just removed a couple print statements	Zachary Sloan

2013-08-15	Removed the markers with no variance (and thus no p-values) from the	Zachary Sloan
	manhattan plot
2013-08-13	Added several test files and the file with the class that	Zachary Sloan
	they import (browser_test.py)
2013-08-07	Fixed things with the dataset dropdowns and mRNA datasets	Zachary Sloan
	Improved the templates for a couple pages related to changing user password, etc
2013-08-02	Fixed a bug related to groups with genofiles (not sure if it makes sense	Zachary Sloan
	for them not to have genofiles yet)
2013-07-30	Just added some print statements to debug an issue with LMM code	Zachary Sloan
	Also added some to notes
2013-07-23	Fixed a couple issues with he quick_search_table.py script	Zachary Sloan
	Added notes on using percona to optimise mysql to gn_installation_notes.txt Started moving "get_trait_data" to DataSet since it is the same regardless of the particular DataSet subclass (PhenotypeDataSet, MrnaAssayDataSet, etc)
2013-07-19	Finished integrating code that reads sample list from geno files	Zachary Sloan
	withouot using reaper and caches results so it doesn't need to read the file every single time someone loads a page
2013-07-19	Created file gen_group_samplelists that iterates through all genofiles	Zachary Sloan
	and builds each groups' samplelist
2013-07-16	Wrote code that can get a dataset's type for every single GN	Zachary Sloan
	dataset; previously we could not view traits in datasets that were not in the DBType table in the database
2013-06-27	Created a group manager page where user administrators can create	Zachary Sloan
	groups of datasets to give/add read privileges to
2013-06-26	Moved code creating DataSets object to a function in dataset.py	Zachary Sloan
	Added caching to creating DataSets object
2013-06-26	Got code that creates DataSets object running	Zachary Sloan
	Fixed one genofile that had extra quotation marks in the comments that caused an error Defaults mb_graph_interval to 1 for species without chromosome lengths in megabases
2013-06-25	Added DataSets class to dataset.py that will be used to create list of	Zachary Sloan
	confidential datasets
2013-06-21	Fixed bug where cursor was still being used in query	Zachary Sloan

2013-06-19	Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flask	Zachary Sloan
	Conflicts: wqflask/base/data_set.py wqflask/wqflask/views.py Fixed a couple conflicts to merge Lei's code related to the correlation page
2013-06-13	Fixed issue where too much memory was used as a result of creating a	Lei Yan
	dataset object for each trait in the correlation results Added new fields/columns for each trait in the correlation result table (max LRS, max LRS location, mean expression) Fixed error if trait doesn't have these fields
2013-06-12	Fixed a couple issues with the template that caused the	Zachary Sloan
	regular search results and show trait page to not display
2013-06-11	Put trait info for correlation results page into a dictionary instead	Lei Yan
	of storing list of GeneralTrait objects Added print statements to track memory usage
2013-05-30	Rewrote some code in get_trait_info in dataset.py	Lei Yan
	Added spearman correlation to show_corr_results and template
2013-05-28	Have correlation values appearing in a table in the template	Lei Yan
	Use scipy to calculate pearson correlation instead of old GN code
2013-05-23	Worked on rewriting the function in data_set.py that gets the sample	Lei Yan
	values for each trait
2013-05-23	Changed the way the query that gets sample ids is generated	Lei Yan

2013-05-23	Now calculates correlation values for traits, but not yet in template	Lei Yan

2013-05-09	Just added some print statements so I can show matrix/vector	Zachary Sloan
	shapes to Tony
2013-05-08	Worked on correlation page	Lei Yan
	Wrote function in dataset.py that gets all the traits in a dataset and their sample values
2013-04-09	Nick's code works fine with human data	Zachary Sloan
	Added option to limit results based on lod score (which also changes the y-axis of the plot)
2013-04-05	Made changes to get pylmm code working with HMDP datasets	Zachary Sloan

2013-04-02	Committing before splitting code that runs pylmm with plink files	Zachary Sloan
	and code that runs it with json
2013-04-02	pylmm code is running for human data (plink .bed genotype files)	Zachary Sloan

2013-03-19	Searches work for the full access human datasets with mRNA assay	Zachary Sloan
	searches, and the trait page can be loaded Need to get marker regression page working with human data now
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