| Age | Commit message (Expand) | Author |
|---|---|---|
| 2014-10-02 | Fixed an error when there's no locus for mRNA expression traits | Zachary Sloan |
| 2014-08-21 | Committer: Lei Yan <lei@penguin.uthsc.edu>•••On branch master | Lei Yan |
| 2014-08-21 | Added the option to display mapping results as either an interval mapping•••or manhattan plot Fixed a few minor bugs | Zachary Sloan |
| 2014-07-21 | Fixed issue where sample values were ordered on the trait page | Zachary Sloan |
| 2014-07-18 | Merge /home/zas1024/gene•••Conflicts: wqflask/base/data_set.py | Lei Yan |
| 2014-07-18 | Added outlier highlighting•••Changed order of tabs in statistics panel on trait page Started working on heatmap | Zachary Sloan |
| 2014-07-18 | Correlation table for phenotypes is working | Lei Yan |
| 2014-07-09 | Updated coffeescript, svg export working fine, interval mapping zoom working | Zachary Sloan |
| 2014-06-25 | Added Karl's correlation matrix code•••Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait | Zachary Sloan |
| 2014-06-06 | Implimented Karl Broman's lodchart code for the interval mapping function.•••Suggestive/significant bars and additive effect curve added | Zachary Sloan |
| 2014-05-05 | Committing a bunch of changes related to integrating GEMMA and•••adding the correlation matrix page | Zachary Sloan |
| 2014-02-28 | Committing after creating AnonCollection class and before adding•••remove trait function | Zachary Sloan |
| 2014-02-28 | Made some changes/comments to Lei's load_genotypes.py file | Zachary Sloan |
| 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 |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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