genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2014-02-28	Made some changes/comments to Lei's load_genotypes.py file	Zachary Sloan

2014-02-27	Began working on a TraitCollection.py file that will contain both the	Zachary Sloan
	object for logged in user collections and collections created by anonymous users.
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
2013-11-27	Clicking a trait in "color by trait" now gets all of its sample values	Zachary Sloan
	that will be used to color the bar graph
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

2013-11-01	Merge /home/sam/gene	Zachary Sloan

2013-10-30	More work on collections	Sam

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
2013-09-27	Added trait links to correlation results	Lei Yan
	Began adding the code that does the initial sort by literature correlation
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).
2013-09-24	Fixed the db_tools import in mrna_assay_tissue_data.py	Zachary Sloan
	Added file for the interval mapping page and wrote code that gets/sets some parameters
2013-09-20	Tissue correlation results work for sample r/rho correlation page	Lei Yan
	and are written to the template
2013-09-13	Merge https://github.com/zsloan/genenetwork	Lei Yan
	Resolved conflicts: wqflask/base/trait.py wqflask/wqflask/correlation/correlationFunction.py wqflask/wqflask/correlation/correlation_function.py wqflask/wqflask/correlation/correlation_functions.py wqflask/wqflask/correlation/show_corr_results.py
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
2013-07-18	Added Amelie's rat data genotypes	Zachary Sloan
	Got human mapping mostly working Fixed dataset dropdown menus
2013-07-18	Merge branch 'master' of https://github.com/zsloan/genenetwork	Zachary Sloan
	Conflicts: wqflask/base/webqtlConfigLocal.py wqflask/maintenance/gen_select_dataset.py wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
2013-07-18	Added to installation notes	Zachary Sloan
	Removed webqtlConfigLocal file containing passwords Updated main page dropdown menus (dataset_menu_structure.json)
2013-07-17	Fixed gen_select_dataset.py	Zachary Sloan
	Appended redis installation info to notes
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
2013-07-12	Rewrote code related to getting the tissue correlation column to display	Lei Yan
	Created new files for mrna assay tissue data and commonly used db query related functions
2013-07-03	Merge /home/zas1024/gene	Lei Yan

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
2013-06-25	Merge git://github.com/zsloan/genenetwork into flask	Lei Yan

2013-06-21	Fixed bug where cursor was still being used in query	Zachary Sloan

2013-06-20	Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flask	Zachary Sloan
	Conflicts: wqflask/requirements.txt wqflask/wqflask/correlation/show_corr_results.py
2013-06-19	Moved the normalize_values function to separate file corr_result_helpers.py	Lei Yan
	Added docstring test to normalize_values Number of overlapping samples column now displays correctly in the correlation results page
2013-06-19	Fixed issue where the Mean Expr, Max LRS, and Max LRS Location columns	Lei Yan
	in the correlation page weren't displaying
2013-06-19	Merge branch 'flask' of git://github.com/zsloan/genenetwork into flask	Lei Yan
	Conflicts: wqflask/base/data_set.py
2013-06-19	Changed QTL parameter name to "get_qtl_info" on trait.py and	Lei Yan
	other places it's called, like search_results.py Added other trait info fields to correlation results page