| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | |||
| 2013-03-19 | Searches work for the full access human datasets with mRNA assay | Zachary Sloan | |
| searches, and the trait page can be loaded Need to get marker regression page working with human data now | |||
| 2013-03-15 | Began work with implementing general search | Zachary Sloan | |
| 2013-03-15 | Changes related to searching for selected points in marker regression plot | Zachary Sloan | |
| 2013-03-13 | Merge branch 'flask' of http://github.com/zsloan/genenetwork into flask | Zachary Sloan | |
| 2013-03-13 | Added some to notes | Zachary Sloan | |
| 2013-03-12 | Added the script generating probesetfreeze data matrix files | Zachary Sloan | |
| The script was created to regenerate a bad file for Evan | |||
| 2013-03-12 | Highlighting points works in Firefox but still doesn't work in chrome | Zachary Sloan | |
| Also noticed issue with chromosome ordering in Firefox | |||
| 2013-03-12 | Got cashing working with pickle | Zachary Sloan | |
| 2013-03-09 | Trying to get caching working with pickle now | Zachary Sloan | |
| 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 | Have first 45% of progress bar working | Zachary Sloan | |
| Changed "threaded" to True in runserver.py; this fixed issue related to getting progress bar to work | |||
| 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 | |||
| 2013-03-06 | Improved positioning/size of copy/print/save buttons for | Zachary Sloan | |
| marker regression table | |||
| 2013-03-05 | Implemented DataTables; there are now options to download the marker | Zachary Sloan | |
| regression result table in various formats | |||
| 2013-03-02 | Created generate_probesetfreeze_file to create the | Zachary Sloan | |
| "probesetfreeze data matrix" file corresponding with the muscle dataset Evan was having trouble with | |||
| 2013-02-28 | Updated benchmark.py to aggregate run times when you run the | Zachary Sloan | |
| operation(s) multiple times | |||
| 2013-02-28 | Added benchmark.py that compares the time of various operations | Zachary Sloan | |
| and gives a report with the percent of total computation time each takes | |||
| 2013-02-28 | Chromosome labels on marker regression plot are centered | Zachary Sloan | |
| Tick marks are now correct and in intervals of 25 for each chromosome | |||
| 2013-02-23 | A static progress bar now displays when loading the marker regression results | Zachary Sloan | |
| 2013-02-22 | Added some to notes | Zachary Sloan | |
| 2013-02-21 | Added underscore.js | Zachary Sloan | |
| 2013-02-21 | Add my_pylmm package | Zachary Sloan | |
| 2013-02-21 | Plot points and chromosome lines are now correct | Zachary Sloan | |
| 2013-02-20 | Did more work with manhattan plot, trying to fix a small issue | Zachary Sloan | |
| with the location of points on the x-axis | |||
| 2013-02-20 | Created y-axis | Zachary Sloan | |
| Split create_graph into many functions Added a buffer to the x and y dimensions in order to add tick labels for the x and y axis | |||
| 2013-02-19 | Manhattan plot and chromosome lines are all correct now | Zachary Sloan | |
| Hovering over a point automatically searches for its corresponding marker in the data table Added headers for the plot and table | |||
| 2013-02-19 | Made lines for manhattan plot proportional to chromosome lengths | Zachary Sloan | |
| 2013-02-15 | Points are labeled with marker names and hovering causes the LRS | Zachary Sloan | |
| value to appear above the plot | |||
| 2013-02-15 | Made it to where hovering over a point in the manhattan plot changes | Zachary Sloan | |
| its style | |||
| 2013-02-15 | Created lines in marker regression scatter plot separating | Zachary Sloan | |
| chromosomes | |||
| 2013-02-14 | Put coffeescript code for manhattan plot into a class/functions | Zachary Sloan | |
| 2013-02-14 | Have marker regression results displaying as a scatterplot (just the points) | Zachary Sloan | |
| using d3.js | |||
| 2013-02-13 | Got results displaying for BXD and fixed genofile_parser.py to work | Zachary Sloan | |
| for all of our genofiles | |||
| 2013-02-13 | Got results for marker regression page displaying in table | Zachary Sloan | |
| 2013-02-13 | Fixed some bugs related to getting the marker regression page working | Zachary Sloan | |
| with Nick's code | |||
| 2013-02-12 | Edited marker_regression.py and data_set.py to store the p-values | Zachary Sloan | |
| and their corresponding markers to be used in the table of qtl results and other figures | |||
| 2013-02-08 | Converted .geno files to json files and wrote code in marker_regression.py | Zachary Sloan | |
| that loads the json files, converts them into the relevant numpy arrays, and passes them into Nick's code (which is returning results that may or may not be correct, but is at least running) | |||
| 2013-02-07 | Added code to marker_regression.py that creates the numpy arrays to | Zachary Sloan | |
| pass to Nick's code and changed the prep_data.py code to operate on a list of phenotype values instead of a textfile with the values delimited | |||
| 2013-02-06 | Edited genofile_parser.py to go through all genofiles and convert | Zachary Sloan | |
| them to the format used by nick's code | |||
| 2013-02-06 | Added changes to example.py and prep_data.py that lets nick's code read in | Zachary Sloan | |
| our data | |||
| 2013-02-06 | Small change to search_results.py to get search results page to work | Zachary Sloan | |
| 2013-01-31 | Added wqflask-nginx.conf | Zachary Sloan | |
| 2013-01-31 | Copied over nginx.conf from /etc/nginx | Zachary Sloan | |
| 2013-01-31 | Merge branch 'flask' of https://github.com/zsloan/genenetwork into flask | Zachary Sloan | |
| 2013-01-31 | Changed reference to 'dataset_name' in keywords to 'dataset' to get | Zachary Sloan | |
| page to work, but will change all references to the dataset name to 'dataset_name' in future to avoid confusion between the dataset name and the actual dataset object | |||
 |
index : genenetwork2 | |
| GeneNetwork (2nd generation) |
| aboutsummaryrefslogtreecommitdiff |