genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2016-04-20	trasnform to transform	DannyArends

2016-04-20	Changed the file stem of generated pictures to CTL	DannyArends

2016-04-20	Adding small figures per trait, so that users can see CTL and QTL for each ↵	DannyArends
	individual phenotype
2016-04-20	Adding parameters, and passing them to the CTL algorithm	DannyArends

2016-04-20	Working on the output template of CTL	DannyArends

2016-04-20	Updates to the CTL code adding the significant results to the result object	DannyArends

2016-04-20	Cleaning code, adding comments	DannyArends

2016-04-20	Adding the lineplot image to the output	DannyArends

2016-04-20	Adding code to do initial CTL mapping (working on the BXD)	DannyArends

2016-04-20	Parsing the names of the individuals, and coding H as -999	DannyArends

2016-04-20	Minor changes to the CTL setup template	DannyArends

2016-04-20	Using the geno parser to get/parse the genotypes for the dataset	DannyArends

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