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2016-05-10Merge branch 'master' of github.com:genenetwork/genenetwork2 into merge_zachPjotr Prins
2016-04-29Fixed database link in trait page detailszsloan
2016-04-29Also fixed links in statistics section (for normal probability plot) and ↵zsloan
removed 'target=_blank's
2016-04-29Fixed links in correlation descriptions on trait page and removed ↵zsloan
target=_blank (so will not open in new window unless user specifies) Fixed javascript so description changes when user changes the method and "Type" option is removed for literature correlation
2016-04-29URL: removed _blank from first URLPjotr Prins
2016-04-29Updated mailing list URLPjotr Prins
2016-04-29Plotting: using cairo-png for headless environmentsPjotr Prins
2016-04-29MergePjotr Prins
2016-04-28Added option to export permutation results for mapping pagezsloan
Added data_scale to dataset objects and basic stats table will now check data scale when calculating range Made interval analyst results table work with datatables Changed the appearance of the basic stats table some by giving it a border
2016-04-28Changed the defunct GeneRIF URL to a working Wikipedia URL (whichPjotr Prins
also points to the non-working NCBI link)
2016-04-26Interval mapping: fix font and image pathPjotr Prins
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.
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