Age | Commit message (Collapse) | Author | |
---|---|---|---|
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 | |||
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 | |||
2013-06-21 | 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 | Zachary Sloan | |
Conflicts: wqflask/base/data_set.py wqflask/wqflask/views.py Fixed a couple conflicts to merge Lei's code related to the correlation page | |||
2013-06-13 | Fixed issue where too much memory was used as a result of creating a | Lei Yan | |
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 | |||
2013-06-12 | Fixed a couple issues with the template that caused the | Zachary Sloan | |
regular search results and show trait page to not display | |||
2013-06-11 | Put trait info for correlation results page into a dictionary instead | Lei Yan | |
of storing list of GeneralTrait objects Added print statements to track memory usage | |||
2013-05-30 | Rewrote some code in get_trait_info in dataset.py | Lei Yan | |
Added spearman correlation to show_corr_results and template | |||
2013-05-28 | Have correlation values appearing in a table in the template | Lei Yan | |
Use scipy to calculate pearson correlation instead of old GN code | |||
2013-05-23 | Worked on rewriting the function in data_set.py that gets the sample | Lei Yan | |
values for each trait | |||
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 | Zachary Sloan | |
shapes to Tony | |||
2013-05-08 | Worked on correlation page | Lei Yan | |
Wrote function in dataset.py that gets all the traits in a dataset and their sample values | |||
2013-04-09 | Nick's code works fine with human data | Zachary Sloan | |
Added option to limit results based on lod score (which also changes the y-axis of the plot) | |||
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 | Zachary Sloan | |
and code that runs it with json | |||
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 | Zachary Sloan | |
searches, and the trait page can be loaded Need to get marker regression page working with human data now | |||
2013-03-12 | Got cashing working with pickle | Zachary Sloan | |
2013-03-07 | Progress bar is now completely working | Zachary Sloan | |
Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code | |||
2013-03-02 | Created generate_probesetfreeze_file to create the | Zachary Sloan | |
"probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with | |||
2013-02-14 | Have marker regression results displaying as a scatterplot (just the points) | Zachary Sloan | |
using d3.js | |||
2013-02-13 | Fixed some bugs related to getting the marker regression page working | Zachary Sloan | |
with Nick's code | |||
2013-02-12 | Edited marker_regression.py and data_set.py to store the p-values | Zachary Sloan | |
and their corresponding markers to be used in the table of qtl results and other figures | |||
2013-01-31 | Changed fd to kw in search_results.py, commented out some lines | Zachary Sloan | |
related to fd | |||
2013-01-18 | Renamed CorrelationPage.py to show_corr_results.py | Zachary Sloan | |
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 | |||
2013-01-03 | Began working on marker_regression.py and created Chromosomes class | Zachary Sloan | |
in species.py | |||
2013-01-03 | Created template for marek regression page and made the compute button direct | Zachary Sloan | |
to it added asbolute_import in data_set.py and trait.py Made several minor changes and deleted commented out code in trait.py | |||
2012-12-18 | Created new file species.py and species class object TheSpecies | Zachary Sloan | |
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 | |||
2012-12-06 | Added minimum/maximum to basic statistics table | Zachary Sloan | |
Continued bug-shooting related to getting show_trait running with phenotype traits | |||
2012-12-06 | Got show_trait running again for MrnaAssay traits | Zachary Sloan | |
2012-12-06 | Made many small changes to show_trait/data_set/search_results/trait to | Zachary Sloan | |
remove use of the formData object and cursor | |||
2012-12-05 | Renamed webqtlTrait.py to trait.py | Zachary Sloan | |
Renamed webqtlTrait class to GeneralTrait Began process of removing fd from show_trait.py Created DatasetGroup object in data_set.py (this may end up becoming its own file later if it becomes big enough) |