| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2015-03-23 | Updates to make GN2 work on my version of penguin (ports, and paths) | DannyArends | |
| 2015-03-17 | Converting an absolute path to a relative path | DannyArends | |
| 2015-01-30 | Fixed several bugs | Zachary Sloan | |
| Added legend to bar chart color by trait function Added scatterplot matrix figure Fixed database timeout problem | |||
| 2014-12-12 | Added a additive effect column to search result and collection tables | Zachary Sloan | |
| Fixed the header so that it looks fine when resizing | |||
| 2014-11-17 | Just more changes converting to bootstrap 3 | Zachary Sloan | |
| 2014-10-17 | Added reference, policies, and links pages | Zachary Sloan | |
| Improved the appearance of the header menu and "title bar" | |||
| 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> | Lei Yan | |
| On branch master | |||
| 2014-08-21 | Added the option to display mapping results as either an interval mapping | Zachary Sloan | |
| or manhattan plot Fixed a few minor bugs | |||
| 2014-07-21 | Fixed issue where sample values were ordered on the trait page | Zachary Sloan | |
| 2014-07-18 | Merge /home/zas1024/gene | Lei Yan | |
| Conflicts: wqflask/base/data_set.py | |||
| 2014-07-18 | Added outlier highlighting | Zachary Sloan | |
| Changed order of tabs in statistics panel on trait page Started working on heatmap | |||
| 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 | Zachary Sloan | |
| Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait | |||
| 2014-06-06 | Implimented Karl Broman's lodchart code for the interval mapping function. | Zachary Sloan | |
| Suggestive/significant bars and additive effect curve added | |||
| 2014-05-05 | Committing a bunch of changes related to integrating GEMMA and | Zachary Sloan | |
| adding the correlation matrix page | |||
| 2014-02-28 | Committing after creating AnonCollection class and before adding | Zachary Sloan | |
| remove trait function | |||
| 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 | Zachary Sloan | |
| object for logged in user collections and collections created by anonymous users. | |||
| 2014-01-30 | Most of the work is done towards running lmm.py from the command line | Zachary Sloan | |
| and storing the results in redis | |||
| 2014-01-29 | Limited number of markers in marker regression result table to | Zachary Sloan | |
| 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 | |||
| 2014-01-23 | Histogram is working | Zachary Sloan | |
| Fixed some bug with generating the manhattan plot for the HLC data set | |||
| 2014-01-03 | Wrote some code for the histogram figure | Zachary Sloan | |
| Changed some code in dataset to try and track down the issue with Amelie's file | |||
| 2013-11-27 | Clicking a trait in "color by trait" now gets all of its sample values | Zachary Sloan | |
| that will be used to color the bar graph | |||
| 2013-11-26 | Made some progress towards getting the traits inside a collection to display ↵ | Zachary Sloan | |
| on hover | |||
| 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 | Zachary Sloan | |
| Correlation page now works with Non-BXD (or whatever group) or All Samples options | |||
| 2013-10-11 | Merge /home/lei/gene | Zachary Sloan | |
| Conflicts: wqflask/maintenance/quick_search_table.py | |||
| 2013-10-10 | Almost have correlation working for non-primary strain/group | Lei Yan | |
| 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. | |||
| 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 | |||
| 2013-09-27 | Added trait links to correlation results | Lei Yan | |
| Began adding the code that does the initial sort by literature correlation | |||
| 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). | |||
| 2013-09-24 | Fixed the db_tools import in mrna_assay_tissue_data.py | Zachary Sloan | |
| Added file for the interval mapping page and wrote code that gets/sets some parameters | |||
| 2013-09-20 | Tissue correlation results work for sample r/rho correlation page | Lei Yan | |
| and are written to the template | |||
| 2013-09-13 | Merge https://github.com/zsloan/genenetwork | Lei Yan | |
| 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 | |||
| 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 | |||
 |
index : genenetwork2 | |
| GeneNetwork (2nd generation) |
| aboutsummaryrefslogtreecommitdiff |