| Age | Commit message (Expand) | Author |
|---|
| 2013-10-11 | Merge /home/lei/gene...Conflicts:
wqflask/maintenance/quick_search_table.py
| Zachary Sloan |
| 2013-10-10 | Almost have correlation working for non-primary strain/group...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.
| Lei Yan |
| 2013-10-09 | Improved some of the code related to the correlation page...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
| Lei Yan |
| 2013-10-08 | Literature correlation works when it is selected as the sorted...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.
| Lei Yan |
| 2013-10-08 | Did some work with interval mapping page; will use qtl reaper to do...the mapping, since it is reliable/fast and avoids us having to rewrite
from scratch using something like r/qtl
| Zachary Sloan |
| 2013-09-24 | Did some work towards doing the tissue correlation for all traits...in a dataset (in order to sort by tissue correlation instead of
sample correlation).
| root |
| 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...manhattan plot
| Zachary Sloan |
| 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 |
| 2013-07-16 | 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 |
| 2013-06-19 | 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 | 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 |
| 2013-05-30 | 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 |
| 2013-04-09 | 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 | 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 |
| 2013-02-14 | 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 |
| 2013-01-31 | Changed fd to kw in search_results.py, commented out some lines...related to fd
| Zachary Sloan |
| 2013-01-18 | Renamed CorrelationPage.py to show_corr_results.py...Worked with correlation code; got to the code that
begins to do the actual correlations
Created a function "get_dataset_and_trait" in
the new file "helper_functions.py" because the
code initializing the dataset and trait objects
was repeated in multiple places
| Zachary Sloan |
| 2013-01-03 | Began working on marker_regression.py and created Chromosomes class...in species.py
| Zachary Sloan |
| 2013-01-03 | Created template for marek regression page and made the compute button direct...to it
added asbolute_import in data_set.py and trait.py
Made several minor changes and deleted commented out code in trait.py
| Zachary Sloan |
| 2012-12-18 | Created new file species.py and species class object TheSpecies...Converted html for the mapping tabs to bootstrap and redid html inside of
the Interval Mapping tab
Added text input for # of permutation tests and bootstrap tests
| Zachary Sloan |
| 2012-12-06 | Added minimum/maximum to basic statistics table...Continued bug-shooting related to getting show_trait running
with phenotype traits
| Zachary Sloan |
| 2012-12-06 | Got show_trait running again for MrnaAssay traits | Zachary Sloan |
