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.