| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2015-07-09 | Mapping methods now check for existing genotype files. | zsloan | |
| Currently we still usually get our samplelists from the genofile. This is dumb because it results in us having a bunch of "dummy" genofiles for certain data sets (seems to be mostly human ones). This means that checking for the genofile alone isn't enough to determine if a mapping method should exist for a given group I wrote some code that will instead get the samplelist from the plink .fam file for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy .geno files, but we can't yet do so because it's currently the only place we seem to be storing the sample list for some groups. I also moved gemma into the plink directory to get it out of the git tree. Since it uses the same files as plink, it doesn't make sense for it to be in its own separate directory | |||
| 2015-07-07 | Added index column and changed the way location is displayed for search results | zsloan | |
| 2015-06-29 | Merge pull request #72 from lomereiter/issue69 | zsloan | |
| Fixes #69 | |||
| 2015-06-22 | fixed a few potential security issues | Artem Tarasov | |
| 2015-06-18 | fix all_samples_ordered | Artem Tarasov | |
| move duplicated code into a method, handle the case of missing f1/f12 correctly | |||
| 2015-05-21 | Changed the digits for additive effect and megabases in the search results table | zsloan | |
| 2015-05-13 | combine three similar queries into one | Artem Tarasov | |
| 2015-05-13 | replace multiple tissue queries with a single one | Artem Tarasov | |
| 2015-05-13 | cache datasets for each group | Artem Tarasov | |
| 2015-05-11 | Moved chunks | Pjotr Prins | |
| 2015-05-11 | Moving pylmm out of the tree | pjotrp | |
| 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" | |||
| 2014-08-21 | 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 | |||
| 2014-07-18 | 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 | |||
| 2014-01-30 | 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 | |||
| 2013-11-26 | 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 | |
| 2013-10-25 | 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 | |||
| 2013-09-24 | 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 | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
| aboutsummaryrefslogtreecommitdiff |