| Age | Commit message (Expand) | Author |
|---|---|---|
| 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 |
| 2013-04-11 | Fixed a bug with quick_search_table.py...Edited generate_probesetfreeze_file.py to try running it on the dataset with incorrect regression lines | Zachary Sloan |
| 2013-04-10 | Created template for quick search page...Fixed a couple bugs with quick_search_table.py | Zachary Sloan |
| 2013-04-09 | Have quick search working for phenotypes | 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 | Made change to nginx config file that seems to have fixed the...504 gateway timeout issue with the human datasets | 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 |
| 2013-04-05 | Made changes to get pylmm code working with HMDP datasets | 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 | Committing before splitting code that runs pylmm with plink files...and code that runs it with json | Zachary Sloan |
| 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...table, but will need to check later to make sure | Zachary Sloan |
| 2013-03-28 | quick_search_table.py now seems to run correctly for ProbeSetXRef...rows | Zachary Sloan |
| 2013-03-28 | Committing before putting quick_search_table code in classes | Zachary Sloan |
| 2013-03-27 | Got quick_search_table.py to a point where it runs; will...know tomorrow whether it ran correctly or not | Zachary Sloan |
| 2013-03-27 | Worked on trying to get results for quick search to display | Zachary Sloan |
| 2013-03-26 | Continued working on quick_search_table.py, which now gets...all of the terms from the ProbeSet table to be included in the quick search | Zachary Sloan |
| 2013-03-26 | Created quick_search_table.py to create table with all of the...information needed for the the quick search features (which searches across all datasets) | Zachary Sloan |
| 2013-03-26 | Just checking in code while in the process of trying to get...the quick search working properly | Zachary Sloan |
| 2013-03-22 | Began creating templates for login/registration | Zachary Sloan |
| 2013-03-22 | Added secure_server.py...Updated notes.txt | Zachary Sloan |
| 2013-03-22 | Removed zach_settings.py from git tracking...Changed mysql password as a result of it being up on git before | Zachary Sloan |
| 2013-03-21 | Did some work towards getting Nick's code working with our plink...human genotype files Tried to get the automatic searches working when points are highlighted on the marker regression manhattan plot | Zachary Sloan |
| 2013-03-19 | In the process of trying to use Nick's pylmmKinship.py code to...precompute the kinship matrix for the human datasets we have plink .bed genotype data for | Zachary Sloan |
| 2013-03-19 | Added Nick's input.py file which uses plink .ped files as input...for his pylmm code | Zachary Sloan |
| 2013-03-19 | Searches work for the full access human datasets with mRNA assay...searches, and the trait page can be loaded Need to get marker regression page working with human data now | Zachary Sloan |
| 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...The script was created to regenerate a bad file for Evan | Zachary Sloan |
| 2013-03-12 | Highlighting points works in Firefox but still doesn't work in chrome...Also noticed issue with chromosome ordering in Firefox | Zachary Sloan |
| 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...Still need to figure out the problem that occurred with negative p-values after I refactored the LMM code | Zachary Sloan |
 |
index : genenetwork2 | |
| GeneNetwork (2nd generation) |
| aboutsummaryrefslogtreecommitdiff |