| Age | Commit message (Expand) | Author |
|---|
| 2014-01-29 | Limited number of markers in marker regression result table to•••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
| Zachary Sloan |
| 2014-01-23 | Histogram is working•••Fixed some bug with generating the manhattan plot for the HLC data set
| Zachary Sloan |
| 2014-01-03 | Wrote some code for the histogram figure•••Changed some code in dataset to try and track down the issue with Amelie's file
| Zachary Sloan |
| 2013-11-26 | Made some progress towards getting the traits inside a collection to display ... | Zachary Sloan |
| 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•••Correlation page now works with Non-BXD (or whatever group)
or All Samples options
| Zachary Sloan |
| 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 |
