| Age | Commit message (Expand) | Author |
|---|---|---|
| 2015-03-05 | Check command | Pjotr Prins |
| 2015-03-05 | Kinship 1.0 parser | Pjotr Prins |
| 2015-02-11 | Added pop-up for empty searches...Replaced pyLMM code with one version of Pyotr's updated faster code Began fixing search to work for combined searches Made login screen look better and fixed for empty fields | Zachary Sloan |
| 2014-07-09 | Updated coffeescript, svg export working fine, interval mapping zoom working | Zachary Sloan |
| 2014-06-25 | Added Karl's correlation matrix code...Improved the "scatterplot matrix" feature on the trait page so that it matches the chosen trait against every selected trait | Zachary Sloan |
| 2014-05-05 | Committing a bunch of changes related to integrating GEMMA and...adding the correlation matrix page | Zachary Sloan |
| 2014-03-26 | Got anonymous collections working correctly...Got results for the HSNIH and CANDLE marker regression pages (still some issues with the manhattan plot) | Zachary Sloan |
| 2014-02-28 | Made some changes/comments to Lei's load_genotypes.py file | Zachary Sloan |
| 2014-02-24 | Chromosome zoom is working for the marker regression manhattan plot...and results show up correctly in the table again | Zachary Sloan |
| 2014-01-30 | The calculations for the manhattan plot are now run from the command...line as a background process, allowing multiple to be run at the same time without the time increasing. | Zachary Sloan |
| 2014-01-30 | Most of the work is done towards running lmm.py from the command line...and storing the results in redis | Zachary Sloan |
| 2014-01-29 | Limited number of markers in marker regression result table to...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 | Zachary Sloan |
| 2014-01-24 | Added natural sort to sort the index column for the sample data in...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 | Zachary Sloan |
| 2014-01-23 | Histogram is working...Fixed some bug with generating the manhattan plot for the HLC data set | Zachary Sloan |
| 2014-01-03 | Wrote some code for the histogram figure...Changed some code in dataset to try and track down the issue with Amelie's file | Zachary Sloan |
| 2013-12-30 | Fixed issue where box plots initially appeared below the bar chart...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. | Zachary Sloan |
| 2013-12-05 | Interval map graph now works properly...Tried to export trait data for "color by trait" function | Zachary Sloan |
| 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...manhattan plot | Zachary Sloan |
| 2013-08-14 | Made some changes related to getting marker regression working for...some datasets | Zachary Sloan |
| 2013-08-07 | Fixed things with the dataset dropdowns and mRNA datasets...Improved the templates for a couple pages related to changing user password, etc | Zachary Sloan |
| 2013-07-30 | Just added some print statements to debug an issue with LMM code...Also added some to notes | Zachary Sloan |
| 2013-07-23 | Fixed a couple issues with he quick_search_table.py script...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) | Zachary Sloan |
| 2013-07-18 | Added Amelie's rat data genotypes...Got human mapping mostly working Fixed dataset dropdown menus | Zachary Sloan |
| 2013-05-31 | Fixed the location column for the quick search page...Began writing some jquery to automatically open the first tab within each species tab on the quick search page (not done yet) | Zachary Sloan |
| 2013-05-09 | Just added some print statements so I can show matrix/vector...shapes to Tony | Zachary Sloan |
| 2013-05-02 | Got quick search code running (but not displaying properly)...Code that processes subset of snps works, in process of putting into a class | Zachary Sloan |
| 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 st......Continued work on file that processes each individual chunk of the snp iterator/plink input | Zachary Sloan |
| 2013-04-24 | Began writing code that writes some objects used in LMM to redis...and writes/reads eachitem in the plink_input | Zachary Sloan |
| 2013-04-23 | Created file correlation_plot.py for the correlation scatterplot...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 | Zachary Sloan |
| 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...we might decide to store it differently | Zachary Sloan |
| 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...for HLC datasets Still need to read in file | Zachary Sloan |
| 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...chunks algorithms' accuracy/speed | Zachary Sloan |
| 2013-04-17 | Wrote code that tests the effectiveness of the function that divides a...list into a given number of chunks | Zachary Sloan |
| 2013-04-17 | Fixed small issue with the divide_into_chunks function...that caused one too many chunks to be created | Zachary Sloan |
| 2013-04-16 | Wrote functions that divide a list into a specified number of chunks...(to be used on the list of snps for the LMM code) | Zachary Sloan |
| 2013-04-16 | Checking in before making some changes | Zachary Sloan |
| 2013-04-16 | Put most of the code calculating human association statistics in...lmm.py into a separate function | Zachary Sloan |
| 2013-04-09 | Nick's code works fine with human data...Added option to limit results based on lod score (which also changes the y-axis of the plot) | Zachary Sloan |
| 2013-04-05 | Loading bar now correctly shows the time to completion...and the code seems to run correctly | Zachary Sloan |
| 2013-04-05 | Got Nick's code working with the MDP datasets under the BXD group,...but with only BXD strains | Zachary Sloan |
| 2013-04-02 | Finished adding code that uses the plink genotype data if...a human dataset and json data if any other species | Zachary Sloan |
| 2013-04-02 | pylmm code is running for human data (plink .bed genotype files) | Zachary Sloan |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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