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AgeCommit message (Expand)Author
2014-02-28Committing after creating AnonCollection class and before adding...remove trait function Zachary Sloan
2014-02-28Made some changes/comments to Lei's load_genotypes.py fileZachary Sloan
2014-02-27Began 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
2014-01-30Most of the work is done towards running lmm.py from the command line...and storing the results in redis Zachary Sloan
2014-01-29Limited 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
2014-01-23Histogram is working...Fixed some bug with generating the manhattan plot for the HLC data set Zachary Sloan
2014-01-03Wrote some code for the histogram figure...Changed some code in dataset to try and track down the issue with Amelie's file Zachary Sloan
2013-11-27Clicking a trait in "color by trait" now gets all of its sample values...that will be used to color the bar graph Zachary Sloan
2013-11-26Made some progress towards getting the traits inside a collection to display ...Zachary Sloan
2013-11-25Got the interval mapping results into a tableZachary Sloan
2013-11-01Merge /home/sam/geneZachary Sloan
2013-10-30More work on collectionsSam
2013-10-25Began working on color coding bar chart by extra attributesZachary Sloan
2013-10-15Changed templates to call the header macro...Correlation page now works with Non-BXD (or whatever group) or All Samples options Zachary Sloan
2013-10-11Merge /home/lei/gene...Conflicts: wqflask/maintenance/quick_search_table.py Zachary Sloan
2013-10-10Almost 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
2013-10-09Improved 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
2013-10-08Literature 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
2013-10-08Did 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
2013-09-27Added trait links to correlation results...Began adding the code that does the initial sort by literature correlation Lei Yan
2013-09-24Did 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
2013-09-24Fixed 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
2013-09-20Tissue correlation results work for sample r/rho correlation page...and are written to the template Lei Yan
2013-09-13Merge 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
2013-08-21Just removed a couple print statementsZachary Sloan
2013-08-15Removed the markers with no variance (and thus no p-values) from the...manhattan plot Zachary Sloan
2013-08-13Added several test files and the file with the class that...they import (browser_test.py) Zachary Sloan
2013-08-07Fixed things with the dataset dropdowns and mRNA datasets...Improved the templates for a couple pages related to changing user password, etc Zachary Sloan
2013-08-02Fixed a bug related to groups with genofiles (not sure if it makes sense...for them not to have genofiles yet) Zachary Sloan
2013-07-30Just added some print statements to debug an issue with LMM code...Also added some to notes Zachary Sloan
2013-07-23Fixed 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
2013-07-19Finished 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
2013-07-19Created file gen_group_samplelists that iterates through all genofiles...and builds each groups' samplelist Zachary Sloan
2013-07-18Added Amelie's rat data genotypes...Got human mapping mostly working Fixed dataset dropdown menus Zachary Sloan
2013-07-18Merge 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
2013-07-18Added to installation notes...Removed webqtlConfigLocal file containing passwords Updated main page dropdown menus (dataset_menu_structure.json) Zachary Sloan
2013-07-17Fixed gen_select_dataset.py...Appended redis installation info to notes Zachary Sloan
2013-07-16Wrote 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
2013-07-12Rewrote 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
2013-07-03Merge /home/zas1024/geneLei Yan
2013-06-27Created a group manager page where user administrators can create...groups of datasets to give/add read privileges to Zachary Sloan
2013-06-26Moved code creating DataSets object to a function in dataset.py...Added caching to creating DataSets object Zachary Sloan
2013-06-26Got 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
2013-06-25Added DataSets class to dataset.py that will be used to create list of...confidential datasets Zachary Sloan
2013-06-25Merge git://github.com/zsloan/genenetwork into flaskLei Yan
2013-06-21Fixed bug where cursor was still being used in queryZachary Sloan
2013-06-20Merge branch 'flask' of git://github.com/leiyan/GeneNetwork2-Python into flask...Conflicts: wqflask/requirements.txt wqflask/wqflask/correlation/show_corr_results.py Zachary Sloan
2013-06-19Moved 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
2013-06-19Fixed issue where the Mean Expr, Max LRS, and Max LRS Location columns...in the correlation page weren't displaying Lei Yan
2013-06-19Merge branch 'flask' of git://github.com/zsloan/genenetwork into flask...Conflicts: wqflask/base/data_set.py Lei Yan
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