genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2015-07-10	Fixed the genofile_parser.py script since some .geno files had been ↵	zsloan
	incorrectly converted to json Fixed GO search to work with combined searches
2015-07-09	Mapping methods now check for existing genotype files.	zsloan
	Currently we still usually get our samplelists from the genofile. This is dumb because it results in us having a bunch of "dummy" genofiles for certain data sets (seems to be mostly human ones). This means that checking for the genofile alone isn't enough to determine if a mapping method should exist for a given group I wrote some code that will instead get the samplelist from the plink .fam file for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy .geno files, but we can't yet do so because it's currently the only place we seem to be storing the sample list for some groups. I also moved gemma into the plink directory to get it out of the git tree. Since it uses the same files as plink, it doesn't make sense for it to be in its own separate directory
2015-07-07	Added index column and changed the way location is displayed for search results	zsloan

2015-06-29	Merge pull request #72 from lomereiter/issue69	zsloan
	Fixes #69
2015-06-22	fixed a few potential security issues	Artem Tarasov

2015-06-18	fix all_samples_ordered	Artem Tarasov
	move duplicated code into a method, handle the case of missing f1/f12 correctly
2015-05-21	Changed the digits for additive effect and megabases in the search results table	zsloan

2015-05-13	combine three similar queries into one	Artem Tarasov

2015-05-13	replace multiple tissue queries with a single one	Artem Tarasov

2015-05-13	cache datasets for each group	Artem Tarasov

2015-05-11	Moved chunks	Pjotr Prins

2015-05-11	Moving pylmm out of the tree	pjotrp

2015-03-17	Converting an absolute path to a relative path	DannyArends

2015-01-30	Fixed several bugs	Zachary Sloan
	Added legend to bar chart color by trait function Added scatterplot matrix figure Fixed database timeout problem
2014-12-12	Added a additive effect column to search result and collection tables	Zachary Sloan
	Fixed the header so that it looks fine when resizing
2014-11-17	Just more changes converting to bootstrap 3	Zachary Sloan

2014-10-17	Added reference, policies, and links pages	Zachary Sloan
	Improved the appearance of the header menu and "title bar"
2014-08-21	Committer: Lei Yan <lei@penguin.uthsc.edu>	Lei Yan
	On branch master
2014-08-21	Added the option to display mapping results as either an interval mapping	Zachary Sloan
	or manhattan plot Fixed a few minor bugs
2014-07-18	Merge /home/zas1024/gene	Lei Yan
	Conflicts: wqflask/base/data_set.py
2014-07-18	Added outlier highlighting	Zachary Sloan
	Changed order of tabs in statistics panel on trait page Started working on heatmap
2014-07-18	Correlation table for phenotypes is working	Lei Yan

2014-07-09	Updated coffeescript, svg export working fine, interval mapping zoom working	Zachary Sloan

2014-06-25	Added Karl's correlation matrix code	Zachary Sloan
	Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait
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