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2016-04-26Merging with Zach's latest branchPjotr Prins
2016-04-25Interval Analyst table mostly working, just need to work out a few more thingszsloan
2016-04-22Fixed issue where manhattan plot setting wasn't being carried over to single ↵zsloan
chromosome view for mapping results Removed a useless "if 1 == 1" line that was in marker_regression_gn1.py for testing.
2016-04-20Interval Mapping now correctly does interval mapping if Marker Regression ↵zsloan
isn't checked (it used to just "connect the dots" of the marker regression output) Changed "Manhattan Plot" label to "Marker Regr." to accurately reflect what the option does
2016-04-20Added borders to stats table in trait pagezsloan
2016-04-20Fix typoPjotr Prins
2016-04-20A few fixes to get the webserver running againPjotr Prins
2016-04-20Add filePjotr Prins
2016-04-20trasnform to transformDannyArends
2016-04-20Changed the file stem of generated pictures to CTLDannyArends
2016-04-20Adding small figures per trait, so that users can see CTL and QTL for each ↵DannyArends
individual phenotype
2016-04-20Adding parameters, and passing them to the CTL algorithmDannyArends
2016-04-20Working on the output template of CTLDannyArends
2016-04-20Updates to the CTL code adding the significant results to the result objectDannyArends
2016-04-20Cleaning code, adding commentsDannyArends
2016-04-20Adding the lineplot image to the outputDannyArends
2016-04-20Adding code to do initial CTL mapping (working on the BXD)DannyArends
2016-04-20Parsing the names of the individuals, and coding H as -999DannyArends
2016-04-20Minor changes to the CTL setup templateDannyArends
2016-04-20Using the geno parser to get/parse the genotypes for the datasetDannyArends
2016-04-20Adding the geno file parser from ZachDannyArends
2016-04-20Creating the analysis object and passing results to the results templateDannyArends
2016-04-20[PATCH 082/100] Testing passing information between the templatesDannyArends
2016-04-20Loading the library and mapping the scan functionDannyArends
2016-04-20Connecting the CTL analysis to the collection overview, by adding a buttonDannyArends
2016-04-20Adding initial file to perform CTL analysisDannyArends
2016-04-20[PATCH 078/100] Adding empty templates for CTL in GN2DannyArends
2016-04-20Cleaning up the WGCNA parameter input templateDannyArends
2016-04-20[PATCH 061/100] Put R/qtl .cross file in TMPDIRPjotr Prins
2016-04-20Show error when GENODIR is missingPjotr Prins
2016-04-20Remove dbdocpjotrp
2016-04-20Removed symlinkspjotrp
2016-04-20r-wgcna: Fix pathspjotrp
2016-04-20More hard-codedpjotrp
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: removalPjotr Prins
2016-04-20[PATCH 047/100] This commit moves the image generation dir *outside* the git ↵Pjotr Prins
repository.
2016-04-20external program should fail on return value not zeropjotrp
2016-04-20[PATCH 045/100] Reverted on previous changes. With a correctedPjotr 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.
2016-04-20Minor fixespjotrp
2016-04-20[PATCH 042/100] Sanitizing locationsPjotr Prins
2016-04-20[PATCH 041/100] Fixes for running toolsPjotr Prins
2016-04-20When 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-aPjotr Prins
[PATCH 039/100] Removing commented code
2016-04-20-aPjotr Prins
[PATCH 038/100] Fix compile errors
2016-04-20[PATCH 037/100] WebQtlConfig: sanitizing naming and used varsPjotr Prins
2016-04-20Settled on the _COMMAND syntax over _RUNpjotrp
2016-04-20With missing samples to not add them to the result setpjotrp
2016-04-20This 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 searchingPjotr Prins
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