| Age | Commit message (Expand) | Author |
|---|
| 2013-08-13 | Added several test files and the file with the class that...they import (browser_test.py)
| Zachary Sloan |
| 2013-08-07 | Fixed things with the dataset dropdowns and mRNA datasets...Improved the templates for a couple pages related to changing user
password, etc
| Zachary Sloan |
| 2013-08-02 | Fixed a bug related to groups with genofiles (not sure if it makes sense...for them not to have genofiles yet)
| Zachary Sloan |
| 2013-07-30 | Just added some print statements to debug an issue with LMM code...Also added some to notes
| Zachary Sloan |
| 2013-07-23 | Fixed a couple issues with he quick_search_table.py script...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)
| Zachary Sloan |
| 2013-07-19 | Finished integrating code that reads sample list from geno files...withouot using reaper and caches results so it doesn't need
to read the file every single time someone loads a page
| Zachary Sloan |
| 2013-07-19 | Created file gen_group_samplelists that iterates through all genofiles...and builds each groups' samplelist
| Zachary Sloan |
| 2013-07-18 | Added Amelie's rat data genotypes...Got human mapping mostly working
Fixed dataset dropdown menus
| Zachary Sloan |
| 2013-07-18 | Merge branch 'master' of https://github.com/zsloan/genenetwork...Conflicts:
wqflask/base/webqtlConfigLocal.py
wqflask/maintenance/gen_select_dataset.py
wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
| Zachary Sloan |
| 2013-07-18 | Added to installation notes...Removed webqtlConfigLocal file containing passwords
Updated main page dropdown menus (dataset_menu_structure.json)
| Zachary Sloan |
| 2013-07-17 | Fixed gen_select_dataset.py...Appended redis installation info to notes
| Zachary Sloan |
| 2013-07-16 | Wrote code that can get a dataset's type for every single GN...dataset; previously we could not view traits in datasets that
were not in the DBType table in the database
| Zachary Sloan |
| 2013-06-27 | Created a group manager page where user administrators can create...groups of datasets to give/add read privileges to
| Zachary Sloan |
| 2013-06-26 | Moved code creating DataSets object to a function in dataset.py...Added caching to creating DataSets object
| Zachary Sloan |
| 2013-06-26 | Got code that creates DataSets object running...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
| Zachary Sloan |
| 2013-06-25 | Added DataSets class to dataset.py that will be used to create list of...confidential datasets
| Zachary Sloan |
| 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...Conflicts:
wqflask/requirements.txt
wqflask/wqflask/correlation/show_corr_results.py
| Zachary Sloan |
| 2013-06-19 | Fixed issue where the Mean Expr, Max LRS, and Max LRS Location columns...in the correlation page weren't displaying
| Lei Yan |
| 2013-06-19 | Merge branch 'flask' of git://github.com/zsloan/genenetwork into flask...Conflicts:
wqflask/base/data_set.py
| Lei Yan |
| 2013-06-19 | Changed QTL parameter name to "get_qtl_info" on trait.py and...other places it's called, like search_results.py
Added other trait info fields to correlation results page
| Lei Yan |
| 2013-06-19 | Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flask...Conflicts:
wqflask/base/data_set.py
wqflask/wqflask/views.py
Fixed a couple conflicts to merge Lei's code related to the correlation page
| Zachary Sloan |
| 2013-06-13 | Merge /home/sam/gene into flask...Conflicts:
wqflask/wqflask/templates/index_page.html
Merging the code on Sam's branch onto my own
| Zachary Sloan |
| 2013-06-13 | Fixed issue where too much memory was used as a result of creating a...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
| Lei Yan |
| 2013-06-12 | Fixed a couple issues with the template that caused the...regular search results and show trait page to not display
| Zachary Sloan |
| 2013-06-11 | Put trait info for correlation results page into a dictionary instead...of storing list of GeneralTrait objects
Added print statements to track memory usage
| Lei Yan |
| 2013-05-31 | Fixed the location column for the quick search page...Began writing some jquery to automatically open the first tab
within each species tab on the quick search page (not done yet)
| Zachary Sloan |
| 2013-05-30 | Rewrote some code in get_trait_info in dataset.py...Added spearman correlation to show_corr_results and template
| Lei Yan |
| 2013-05-28 | Have correlation values appearing in a table in the template...Use scipy to calculate pearson correlation instead of old GN code
| Lei Yan |
| 2013-05-23 | Worked on rewriting the function in data_set.py that gets the sample...values for each trait
| Lei Yan |
| 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...shapes to Tony
| Zachary Sloan |
| 2013-05-08 | Worked on correlation page...Wrote function in dataset.py that gets all the traits in a dataset
and their sample values
| Lei Yan |
| 2013-04-17 | Created file with pickled SNPIterator (from input.py) data...for HLC datasets
Still need to read in file
| Zachary Sloan |
| 2013-04-09 | Nick's code works fine with human data...Added option to limit results based on lod score (which also
changes the y-axis of the plot)
| Zachary Sloan |
| 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...and code that runs it with json
| Zachary Sloan |
| 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...searches, and the trait page can be loaded
Need to get marker regression page working with human data now
| Zachary Sloan |
| 2013-03-12 | Added the script generating probesetfreeze data matrix files...The script was created to regenerate a bad file for Evan
| Zachary Sloan |
| 2013-03-12 | Got cashing working with pickle | Zachary Sloan |
| 2013-03-07 | Progress bar is now completely working...Still need to figure out the problem that occurred
with negative p-values after I refactored the LMM
code
| Zachary Sloan |
| 2013-03-02 | Created generate_probesetfreeze_file to create the..."probesetfreeze data matrix" file corresponding with the
muscle dataset Evan was having trouble with
| Zachary Sloan |
| 2013-02-22 | Added some to notes | Zachary Sloan |
| 2013-02-14 | Have marker regression results displaying as a scatterplot (just the points)...using d3.js
| Zachary Sloan |
| 2013-02-13 | Fixed some bugs related to getting the marker regression page working...with Nick's code
| Zachary Sloan |
| 2013-02-12 | Edited 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 |
| 2013-02-07 | Added 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 |
| 2013-01-31 | Changed fd to kw in search_results.py, commented out some lines...related to fd
| Zachary Sloan |
