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2014-10-02Fixed an error when there's no locus for mRNA expression traitsZachary Sloan
2014-08-21Committer: Lei Yan <lei@penguin.uthsc.edu>Lei Yan
On branch master
2014-08-21Added the option to display mapping results as either an interval mappingZachary Sloan
or manhattan plot Fixed a few minor bugs
2014-07-21Fixed issue where sample values were ordered on the trait pageZachary Sloan
2014-07-18Merge /home/zas1024/geneLei Yan
Conflicts: wqflask/base/data_set.py
2014-07-18Added outlier highlightingZachary Sloan
Changed order of tabs in statistics panel on trait page Started working on heatmap
2014-07-18Correlation table for phenotypes is workingLei Yan
2014-07-09Updated coffeescript, svg export working fine, interval mapping zoom workingZachary Sloan
2014-06-25Added Karl's correlation matrix codeZachary Sloan
Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait
2014-06-06Implimented Karl Broman's lodchart code for the interval mapping function.Zachary Sloan
Suggestive/significant bars and additive effect curve added
2014-05-05Committing a bunch of changes related to integrating GEMMA andZachary Sloan
adding the correlation matrix page
2014-02-28Committing after creating AnonCollection class and before addingZachary Sloan
remove trait function
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 theZachary Sloan
object for logged in user collections and collections created by anonymous users.
2014-01-30Most of the work is done towards running lmm.py from the command lineZachary Sloan
and storing the results in redis
2014-01-29Limited number of markers in marker regression result table toZachary 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
2014-01-23Histogram is workingZachary Sloan
Fixed some bug with generating the manhattan plot for the HLC data set
2014-01-03Wrote some code for the histogram figureZachary Sloan
Changed some code in dataset to try and track down the issue with Amelie's file
2013-11-27Clicking a trait in "color by trait" now gets all of its sample valuesZachary Sloan
that will be used to color the bar graph
2013-11-26Made some progress towards getting the traits inside a collection to display ↵Zachary Sloan
on hover
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 macroZachary Sloan
Correlation page now works with Non-BXD (or whatever group) or All Samples options
2013-10-11Merge /home/lei/geneZachary Sloan
Conflicts: wqflask/maintenance/quick_search_table.py
2013-10-10Almost have correlation working for non-primary strain/groupLei 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.
2013-10-09Improved some of the code related to the correlation pageLei 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
2013-10-08Literature correlation works when it is selected as the sortedLei 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.
2013-10-08Did some work with interval mapping page; will use qtl reaper to doZachary Sloan
the mapping, since it is reliable/fast and avoids us having to rewrite from scratch using something like r/qtl
2013-09-27Added trait links to correlation resultsLei Yan
Began adding the code that does the initial sort by literature correlation
2013-09-24Did some work towards doing the tissue correlation for all traitsroot
in a dataset (in order to sort by tissue correlation instead of sample correlation).
2013-09-24Fixed the db_tools import in mrna_assay_tissue_data.pyZachary Sloan
Added file for the interval mapping page and wrote code that gets/sets some parameters
2013-09-20Tissue correlation results work for sample r/rho correlation pageLei Yan
and are written to the template
2013-09-13Merge https://github.com/zsloan/genenetworkLei 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
2013-08-21Just removed a couple print statementsZachary Sloan
2013-08-15Removed the markers with no variance (and thus no p-values) from theZachary Sloan
manhattan plot
2013-08-13Added several test files and the file with the class thatZachary Sloan
they import (browser_test.py)
2013-08-07Fixed things with the dataset dropdowns and mRNA datasetsZachary Sloan
Improved the templates for a couple pages related to changing user password, etc
2013-08-02Fixed a bug related to groups with genofiles (not sure if it makes senseZachary Sloan
for them not to have genofiles yet)
2013-07-30Just added some print statements to debug an issue with LMM codeZachary Sloan
Also added some to notes
2013-07-23Fixed a couple issues with he quick_search_table.py scriptZachary 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)
2013-07-19Finished integrating code that reads sample list from geno filesZachary Sloan
withouot using reaper and caches results so it doesn't need to read the file every single time someone loads a page
2013-07-19Created file gen_group_samplelists that iterates through all genofilesZachary Sloan
and builds each groups' samplelist
2013-07-18Added Amelie's rat data genotypesZachary Sloan
Got human mapping mostly working Fixed dataset dropdown menus
2013-07-18Merge branch 'master' of https://github.com/zsloan/genenetworkZachary Sloan
Conflicts: wqflask/base/webqtlConfigLocal.py wqflask/maintenance/gen_select_dataset.py wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
2013-07-18Added to installation notesZachary Sloan
Removed webqtlConfigLocal file containing passwords Updated main page dropdown menus (dataset_menu_structure.json)
2013-07-17Fixed gen_select_dataset.pyZachary Sloan
Appended redis installation info to notes
2013-07-16Wrote code that can get a dataset's type for every single GNZachary Sloan
dataset; previously we could not view traits in datasets that were not in the DBType table in the database
2013-07-12Rewrote code related to getting the tissue correlation column to displayLei Yan
Created new files for mrna assay tissue data and commonly used db query related functions
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 16:22:45 +0000