# 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.