genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2016-04-20	Adding the geno file parser from Zach	DannyArends

2016-04-20	Creating the analysis object and passing results to the results template	DannyArends

2016-04-20	[PATCH 082/100] Testing passing information between the templates	DannyArends

2016-04-20	Loading the library and mapping the scan function	DannyArends

2016-04-20	Connecting the CTL analysis to the collection overview, by adding a button	DannyArends

2016-04-20	Adding initial file to perform CTL analysis	DannyArends

2016-04-20	[PATCH 078/100] Adding empty templates for CTL in GN2	DannyArends

2016-04-20	Cleaning up the WGCNA parameter input template	DannyArends

2016-04-20	[PATCH 061/100] Put R/qtl .cross file in TMPDIR	Pjotr Prins

2016-04-20	Show error when GENODIR is missing	Pjotr Prins

2016-04-20	Remove dbdoc	pjotrp

2016-04-20	Removed symlinks	pjotrp

2016-04-20	r-wgcna: Fix paths	pjotrp

2016-04-20	More hard-coded	pjotrp

2016-04-20	[PATCH 050/100] Using out-of-tree storage. Added comments for plink,	Pjotr Prins
	gemma.
2016-04-20	[PATCH 049/100] SNP_PATH: removal	Pjotr Prins

2016-04-20	[PATCH 047/100] This commit moves the image generation dir outside the git ↵	Pjotr Prins
	repository.
2016-04-20	external program should fail on return value not zero	pjotrp

2016-04-20	[PATCH 045/100] Reverted on previous changes. With a corrected	Pjotr Prins
	python2-piddle module the thing works. Turns out that the version we are using is not the same as the public one. Despite the same version number.
2016-04-20	Minor fixes	pjotrp

2016-04-20	[PATCH 042/100] Sanitizing locations	Pjotr Prins

2016-04-20	[PATCH 041/100] Fixes for running tools	Pjotr Prins

2016-04-20	When a sample does not exist we should not set sample_data to None. Better ↵	pjotrp
	to leave it out so it never gets processed again.
2016-04-20	-a	Pjotr Prins
	[PATCH 039/100] Removing commented code
2016-04-20	-a	Pjotr Prins
	[PATCH 038/100] Fix compile errors
2016-04-20	[PATCH 037/100] WebQtlConfig: sanitizing naming and used vars	Pjotr Prins

2016-04-20	Settled on the _COMMAND syntax over _RUN	pjotrp

2016-04-20	With missing samples to not add them to the result set	pjotrp

2016-04-20	This threw an error when sample is missing in the DB.	pjotrp
	Let sample pass without data if the sample/genotype does not exist in the database.
2016-04-20	[PATCH 033/100] Refactored file searching	Pjotr Prins

2016-04-20	[PATCH 032/100] file locating: error checking is built-in	Pjotr Prins

2016-04-20	Fine tuning file locating	pjotrp

2016-04-20	tools.py: add function locate_without_error	pjotrp

2016-04-20	[PATCH 027/100] Introduce tools.locate	Pjotr Prins

2016-04-20	[PATCH 026/100] Introducing cached values PYLMM_COMMAND,	Pjotr Prins
	GEMMA_COMMAND, PLINK_COMMAND and TEMPDIR
2016-04-20	Introducing TEMPDIR	pjotrp

2016-04-20	[PATCH 024/100] Sanitizing file handling	Pjotr Prins

2016-04-20	[PATCH 023/100] WIP fixing all paths	Pjotr Prins

2016-04-20	Remover dependency to logger_tree (may reintroduce later)	pjotrp

2016-04-20	[PATCH 018/100] Find external tools: refactored code to work with GNU Guix	Pjotr Prins

2016-04-20	Removed import htmlgen as is not used (apparently)	pjotrp

2016-04-18	Additive effect lines are now separated by chromosome (like the qtl line in ↵	zsloan
	the last commit) Fixed order of stats table in trait page Removed the qtl results table from chromosome view; will add the Interval Analyst output later
2016-04-14	Fixed issue where qtl lines in interval mapping wouldn't connect between ↵	zsloan
	chromosomes Added text explaining what * indicates in the mapping options menu Removed ranges (log2 and fold) from stats table for phenotype traits
2016-04-13	Moved the code getting the description/location because it was throwing an ↵	zsloan
	error for phenotype traits
2016-04-13	Global search should be able to return description and location columns now	zsloan

2016-04-11	Changed the way trait data is retrieved for the global search page (it now ↵	zsloan
	gets the LRS location repr and other variables needed to display in table during the retrieve_info function in trait.py instead of retrieve_trait_info in dataset.py) This change increases the speed by a bit (85 seconds to 66 seconds for example) Made the column width for location a bit wider for global search page so it doesn't spill onto a second line
2016-04-07	Added option to change the maximum y-axis value for GN1 mapping figure	zsloan

2016-04-07	Permutation figure and x-axis label should change to correctly reflect the ↵	zsloan
	mapping scale (lrs or lod) Fixed bug where broken image link would appear if you ran R/qtl with no permutations
2016-04-07	SNP Track option should now work for GN1 mapping figure	zsloan
	Fixed typo in show_trait html that caused the p-value slider to not work for correlations
2016-04-06	The option to switch between LRS and LOD for the GN1 mapping figure should ↵	zsloan
	now work correctly. The correct value (LRS or LOD) will now be displayed in the results table Added glossary links for GN1 mapping figure options (permutations, bootstrap, etc)