| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2015-07-10 | Fixed the genofile_parser.py script since some .geno files had been ↵ | zsloan | |
| incorrectly converted to json Fixed GO search to work with combined searches | |||
| 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 | |||
| 2015-07-09 | Some phenotype searches were throwing an error due to an assert statement in ↵ | zsloan | |
| trait.py. Since I couldn't find the purpose of the assert statement I removed it. | |||
| 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 | |||
| 2015-05-26 | Merge pull request #58 from lomereiter/pp | zsloan | |
| Use NVD3 for bar chart and probability plot | |||
| 2015-05-23 | new probability plot (using NVD3 library) | Artem Tarasov | |
| * z scores are computed on the client side (using jStat library) * added Shapiro-Wilk test results | |||
| 2015-05-22 | Fixed issue where correlation didn't work for human traits (and probably ↵ | zsloan | |
| some others) | |||
| 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 | |
| 2015-05-12 | Resolved conflict before commit | zsloan | |
| 2015-05-12 | Fix #35 | Artem Tarasov | |
| * 'aliases' and 'location' are shown only where relevant * descriptions for phenotype datasets are provided at the top | |||
| 2015-05-11 | Moved chunks | Pjotr Prins | |
| 2015-05-11 | Moving pylmm out of the tree | pjotrp | |
| 2015-04-10 | Added git large file system (the .gitattributes files) and fixed an issue ↵ | zsloan | |
| where rat trait pages wouldn't work | |||
| 2015-03-27 | Changed HTMLPATH in webqtlConfig since I forgot to in the last commit (since ↵ | zsloan | |
| it used to point to the now-renamed 'web' directory). It obviously also needs to be renamed later, but I'll have to find every place that calls webqtlConfig.HTMLPATH first to do so. | |||
| 2015-03-26 | Removed several unused files from the base folder and their references in ↵ | zsloan | |
| other files | |||
| 2015-03-25 | Pair scan image now loads properly | zsloan | |
| 2015-03-24 | Change back port location and home directory location; this should be in ↵ | zsloan | |
| external settings | |||
| 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 | |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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