| Age | Commit message (Expand) | Author |
|---|
| 2014-02-27 | Began working on a TraitCollection.py file that will contain both the...object for logged in user collections and collections created by
anonymous users.
| Zachary Sloan |
| 2014-01-30 | Most of the work is done towards running lmm.py from the command line...and storing the results in redis
| Zachary Sloan |
| 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 |
| 2013-11-27 | Clicking a trait in "color by trait" now gets all of its sample values...that will be used to color the bar graph
| 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 |
| 2013-11-01 | 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...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 |
| 2013-09-27 | Added trait links to correlation results...Began adding the code that does the initial sort by literature
correlation
| Lei Yan |
| 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 |
| 2013-09-24 | Fixed the db_tools import in mrna_assay_tissue_data.py...Added file for the interval mapping page and wrote code that
gets/sets some parameters
| Zachary Sloan |
| 2013-09-20 | Tissue correlation results work for sample r/rho correlation page...and are written to the template
| Lei Yan |
| 2013-09-13 | Merge https://github.com/zsloan/genenetwork...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
| Lei Yan |
| 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 |
| 2013-07-18 | 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 |
| 2013-07-12 | Rewrote code related to getting the tissue correlation column to display...Created new files for mrna assay tissue data and commonly used
db query related functions
| Lei Yan |
| 2013-07-03 | Merge /home/zas1024/gene | Lei Yan |
| 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 |
| 2013-06-25 | 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...Conflicts:
wqflask/requirements.txt
wqflask/wqflask/correlation/show_corr_results.py
| Zachary Sloan |
| 2013-06-19 | Moved the normalize_values function to separate file corr_result_helpers.py...Added docstring test to normalize_values
Number of overlapping samples column now displays correctly in the
correlation results page
| Lei Yan |
| 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 |
