| Age | Commit message (Expand) | Author |
|---|
| 2016-03-18 | Replaced header with other information in qtl map...Began adding menu to qtl map
Fixed global search to not retrieve samples (to increase speed)
Got the vector plot working again so it can be displayed alongside the gn1-style plot
Only display the vector plot when doing GEMMA to speed up (this might not be necessary)
| zsloan |
| 2016-03-15 | Fixed the mapping figure track that lets you zoom into a smaller range...Fixed the third party mapping figure tracks to refer to the correct chromosome (before it was always 1)
| zsloan |
| 2016-03-02 | Increased gsearch speed by removing unnecessary query for sample data...Still slower than preferable due to having to query the gn1 database for every trait in the search results
| zsloan |
| 2016-02-04 | Most importantly, this commit fixes an issue that caused the trait page to no......An Intro section is also added to the header, though for the time being its contents aren't populated and the edit option isn't working
| zsloan |
| 2015-11-09 | Fixed issue that caused mapping to not work; for some reason the path to pylm... | zsloan |
| 2015-10-12 | Changed the location filter for correlation page | zsloan |
| 2015-09-11 | Comment out some excessive stdout spam | DannyArends |
| 2015-09-10 | Fixed "TypeError: float argument required, not NoneType" about mean....Committer: Lei Yan <lei@penguin.uthsc.edu>
On branch master
| Lei Yan |
| 2015-08-26 | Fixed issue with colums for the gene global search (still need to change for ......Fixed issue where LRS and LOD are sometimes labeled incorrectly
Changed the header of the trait page
Added link to GN1 in header
Fixxed an issue that made permutations not work with pylmm
Fixed "sign in" button when creating a collection while not logged in
| zsloan |
| 2015-07-20 | Fixed the code that generates the dataset selection drop-down for correlations...Made changes to the tables of correlation results, collections, and search results:
- Added resizeable columns to correlation results and collections, but not to search results
because it seems that it requires Y scrolling to be set (I'll check if it makes sense to add scrolling
to the search results)
- Correlation results and collections are now in scrolling tables
- The style is the same across all of these tables now
Remaining issues:
- It doesn't seem like I can set the column width when initializing dataTables in
correlation results. I don't know why this is; it might be due to the table already being the size
of a full page. I want to be able to default to some good widths, even if the user can resize them
- I tried adding hoverForMore, but it doesn't seem to cooperate with datatable cells; I think this is
due to having to put the text in a div.
| zsloan |
| 2015-07-10 | Fixed the genofile_parser.py script since some .geno files had been incorrect......Fixed GO search to work with combined searches
| zsloan |
| 2015-07-09 | Mapping methods now check for existing genotype files....Currently we still usually get our samplelists from the genofile. This is
dumb because it results in us having a bunch of "dummy" genofiles for certain
data sets (seems to be mostly human ones). This means that checking for the
genofile alone isn't enough to determine if a mapping method should exist
for a given group
I wrote some code that will instead get the samplelist from the plink .fam file
for some of these groups/datasets (if the .fam file exists). Ideally I would like to remove all of the dummy
.geno files, but we can't yet do so because it's currently the only place we seem to be storing
the sample list for some groups.
I also moved gemma into the plink directory to get it out of the git tree.
Since it uses the same files as plink, it doesn't make sense for it
to be in its own separate directory
| zsloan |
| 2015-07-07 | Added index column and changed the way location is displayed for search results | zsloan |
| 2015-06-29 | Merge pull request #72 from lomereiter/issue69...Fixes #69 | zsloan |
| 2015-06-22 | fixed a few potential security issues | Artem Tarasov |
| 2015-06-18 | fix all_samples_ordered...move duplicated code into a method,
handle the case of missing f1/f12 correctly
| Artem Tarasov |
| 2015-05-21 | Changed the digits for additive effect and megabases in the search results table | zsloan |
| 2015-05-13 | combine three similar queries into one | Artem Tarasov |
| 2015-05-13 | replace multiple tissue queries with a single one | Artem Tarasov |
| 2015-05-13 | cache datasets for each group | Artem Tarasov |
| 2015-05-11 | Moved chunks | Pjotr Prins |
| 2015-05-11 | Moving pylmm out of the tree | pjotrp |
| 2015-03-17 | Converting an absolute path to a relative path | DannyArends |
| 2015-01-30 | Fixed several bugs...Added legend to bar chart color by trait function
Added scatterplot matrix figure
Fixed database timeout problem
| Zachary Sloan |
| 2014-12-12 | Added a additive effect column to search result and collection tables...Fixed the header so that it looks fine when resizing
| Zachary Sloan |
| 2014-11-17 | Just more changes converting to bootstrap 3 | Zachary Sloan |
| 2014-10-17 | Added reference, policies, and links pages...Improved the appearance of the header menu and "title bar"
| Zachary Sloan |
| 2014-08-21 | Committer: Lei Yan <lei@penguin.uthsc.edu>...On branch master
| Lei Yan |
| 2014-08-21 | Added the option to display mapping results as either an interval mapping...or manhattan plot
Fixed a few minor bugs
| Zachary Sloan |
| 2014-07-18 | Merge /home/zas1024/gene...Conflicts:
wqflask/base/data_set.py
| Lei Yan |
| 2014-07-18 | Added outlier highlighting...Changed order of tabs in statistics panel on trait page
Started working on heatmap
| Zachary Sloan |
| 2014-07-18 | Correlation table for phenotypes is working | Lei Yan |
| 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 |
| 2014-06-06 | Implimented Karl Broman's lodchart code for the interval mapping function....Suggestive/significant bars and additive effect curve added
| Zachary Sloan |
| 2014-05-05 | Committing a bunch of changes related to integrating GEMMA and...adding the correlation matrix page
| 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 |
| 2014-01-23 | 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 |
| 2013-11-26 | Made some progress towards getting the traits inside a collection to display ... | Zachary Sloan |
| 2013-11-25 | Got the interval mapping results into a table | Zachary Sloan |
| 2013-10-25 | Began working on color coding bar chart by extra attributes | Zachary Sloan |
| 2013-10-15 | Changed templates to call the header macro...Correlation page now works with Non-BXD (or whatever group)
or All Samples options
| Zachary Sloan |
| 2013-10-11 | Merge /home/lei/gene...Conflicts:
wqflask/maintenance/quick_search_table.py
| Zachary Sloan |
| 2013-10-10 | Almost have correlation working for non-primary strain/group...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.
| Lei Yan |
| 2013-10-09 | Improved some of the code related to the correlation page...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
| Lei Yan |
| 2013-10-08 | Literature correlation works when it is selected as the sorted...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.
| Lei Yan |
| 2013-10-08 | Did some work with interval mapping page; will use qtl reaper to do...the mapping, since it is reliable/fast and avoids us having to rewrite
from scratch using something like r/qtl
| Zachary Sloan |
| 2013-09-24 | Did some work towards doing the tissue correlation for all traits...in a dataset (in order to sort by tissue correlation instead of
sample correlation).
| root |
