| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | |||
| 2014-01-24 | Added natural sort to sort the index column for the sample data in | Zachary Sloan | |
| the trait page Hid the Quick Search on the index page until it is working well. Started writing a file to run the pyLMM code in the background to avoid memory issues/timing out | |||
| 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 | |||
| 2013-12-30 | Fixed issue where box plots initially appeared below the bar chart | Zachary Sloan | |
| instead of in the second tab In the process of trying to fix the genofile to json parser so we can map Amelie's rat data In the process of having the color of bars in the bar chart "follow" them when they are resorted. | |||
| 2013-12-05 | Interval map graph now works properly | Zachary Sloan | |
| Tried to export trait data for "color by trait" function | |||
| 2013-09-13 | Added file that will convert genofiles to plink ped/map files | Zachary Sloan | |
| 2013-08-15 | Removed the markers with no variance (and thus no p-values) from the | Zachary Sloan | |
| manhattan plot | |||
| 2013-08-14 | Made some changes related to getting marker regression working for | Zachary Sloan | |
| some datasets | |||
| 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 | |||
| 2013-07-30 | 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) | |||
| 2013-07-18 | Added Amelie's rat data genotypes | Zachary Sloan | |
| Got human mapping mostly working Fixed dataset dropdown menus | |||
| 2013-05-31 | Fixed the location column for the quick search page | Zachary Sloan | |
| Began writing some jquery to automatically open the first tab within each species tab on the quick search page (not done yet) | |||
| 2013-05-09 | Just added some print statements so I can show matrix/vector | Zachary Sloan | |
| shapes to Tony | |||
| 2013-05-02 | Got quick search code running (but not displaying properly) | Zachary Sloan | |
| Code that processes subset of snps works, in process of putting into a class | |||
| 2013-04-30 | Did a little with correlation_plot.py | Zachary Sloan | |
| 2013-04-26 | Added file that checks how much time is added to a loop's runtime by print ↵ | Zachary Sloan | |
| statements Continued work on file that processes each individual chunk of the snp iterator/plink input | |||
| 2013-04-24 | Began writing code that writes some objects used in LMM to redis | Zachary Sloan | |
| and writes/reads eachitem in the plink_input | |||
| 2013-04-23 | Created file correlation_plot.py for the correlation scatterplot | Zachary Sloan | |
| Reverted temp_data.py to previous version that doesn't include the "part" input (for chunks) Made change to lmm related to splitting main iterator into chunks Deleted a bunch of unnecessary commented out code from show_trait.py | |||
| 2013-04-19 | Fixed the issue with the x-axis coordinates for marker regression plot | Zachary Sloan | |
| 2013-04-18 | The plink_input is split into chunks that are stored in temp_data, but | Zachary Sloan | |
| we might decide to store it differently | |||
| 2013-04-18 | LMM code now reads in gzipped pickled plink snp iterator object | Zachary Sloan | |
| 2013-04-18 | input file is now loaded by pickle | Zachary Sloan | |
| 2013-04-17 | Created file with pickled SNPIterator (from input.py) data | Zachary Sloan | |
| for HLC datasets Still need to read in file | |||
| 2013-04-17 | Added a benchmark for running the chunks code on the list of snps | Zachary Sloan | |
| 2013-04-17 | Renamed chunk_test.py to chunks.py | Zachary Sloan | |
| 2013-04-17 | Updated chunk_test.py | Zachary Sloan | |
| 2013-04-17 | Added chunk_test.py which compared my/ and sam's split into | Zachary Sloan | |
| chunks algorithms' accuracy/speed | |||
| 2013-04-17 | Wrote code that tests the effectiveness of the function that divides a | Zachary Sloan | |
| list into a given number of chunks | |||
| 2013-04-17 | Fixed small issue with the divide_into_chunks function | Zachary Sloan | |
| that caused one too many chunks to be created | |||
| 2013-04-16 | Wrote functions that divide a list into a specified number of chunks | Zachary Sloan | |
| (to be used on the list of snps for the LMM code) | |||
| 2013-04-16 | Checking in before making some changes | Zachary Sloan | |
| 2013-04-16 | Put most of the code calculating human association statistics in | Zachary Sloan | |
| lmm.py into a separate function | |||
| 2013-04-09 | Nick's code works fine with human data | Zachary Sloan | |
| Added option to limit results based on lod score (which also changes the y-axis of the plot) | |||
| 2013-04-05 | Loading bar now correctly shows the time to completion | Zachary Sloan | |
| and the code seems to run correctly | |||
| 2013-04-05 | Got Nick's code working with the MDP datasets under the BXD group, | Zachary Sloan | |
| but with only BXD strains | |||
| 2013-04-02 | Finished adding code that uses the plink genotype data if | Zachary Sloan | |
| a human dataset and json data if any other species | |||
| 2013-04-02 | pylmm code is running for human data (plink .bed genotype files) | Zachary Sloan | |
| 2013-03-28 | quick_search_table.py seems to be running OK for the PublishXRef | Zachary Sloan | |
| table, but will need to check later to make sure | |||
| 2013-03-26 | Just checking in code while in the process of trying to get | Zachary Sloan | |
| the quick search working properly | |||
| 2013-03-22 | Removed zach_settings.py from git tracking | Zachary Sloan | |
| Changed mysql password as a result of it being up on git before | |||
| 2013-03-21 | Did some work towards getting Nick's code working with our plink | Zachary Sloan | |
| human genotype files Tried to get the automatic searches working when points are highlighted on the marker regression manhattan plot | |||
| 2013-03-19 | In the process of trying to use Nick's pylmmKinship.py code to | Zachary Sloan | |
| precompute the kinship matrix for the human datasets we have plink .bed genotype data for | |||
| 2013-03-19 | Added Nick's input.py file which uses plink .ped files as input | Zachary Sloan | |
| for his pylmm code | |||
| 2013-03-08 | Caching is working for marker regression but really slowly | Zachary Sloan | |
| 2013-03-08 | Refactored GWAS function in lmm.py | Zachary Sloan | |
| 2013-03-07 | Progress bar is now completely working | Zachary Sloan | |
| Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code | |||
| 2013-03-07 | Created file temp_data to store data related to progress | Zachary Sloan | |
| of the marker regression calculations Storing progress of kinship matrix calculation in variable as portion of 45 (the rough percent of total marker regression calculation time | |||
| 2013-03-06 | Stored percent of calculate_kinship function completion in | Zachary Sloan | |
| variable | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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