local changes stashed - to merge into master later
Merge remote-tracking branch 'upstream/master'
Merge pull request #17 from brian-bot/master

change runEvalGenesets to write out file
Merge pull request #18 from brian-bot/master

fix typos which did not search allDatasets (only core)
Merge pull request #19 from brian-bot/master

updates from JG and parsing of sample names in subtyping calls
Merge pull request #20 from brian-bot/master

improvements for the last minute re-run
Merge pull request #21 from brian-bot/master

summarization of the genesets
Refactor of evaluation pipeline; added TCGA eval
Merged with Bot
Merge pull request #22 from jguinney/master

Refactor
correct scaling of survival times for tcga and kfsyscc