mj163163 / atlantis

Code used for biomarker discovery using party (building conditional random forests)

ATLANTIS

R package for biomarker/depenedency relationship discovery (via learning random forests of conditional inference trees).

There are two packages contained in this directory which are both necessary to run ATLANTIS:

- partyMod: A fork from the party package which is used to actually
  build the model.  The fork was necessary to include tweaks to reduce 
  memory necessary for training with large numbers of input
  features.  (See https://cran.r-project.org/web/packages/party/index.html and
  "Torsten Hothorn, Peter Buehlmann, Sandrine Dudoit, Annette Molinaro and 
  Mark Van Der Laan (2006). Survival Ensembles. Biostatistics, 7(3),
  355--373.)

- ATLANTIS: The wrapper around party which was used to learn the models
  for the paper "Defining a Cancer Dependency Map".  Includes some prefiltering
  of features and biased weights more heavily on sensitive lines.   See 
  the paper for more details on the specific settings used for each MDP
  class.