Ben Lengerich

Software

My research code is avilable on Github. These include:

  • scContextualized provides utilities for contextualized analysis of biological data, scaling to the requirements of large single-cell datasets.
  • Contextualized unifies all sorts of context-specific analysis including context-specific regression, context-specific correlation and context-specific networks for analysis of heterogeneous populations.
  • EBM_Utils provides utilities functions for Explainable Boosting Machines.
  • Interpret (from MSR) is a package for interpretable machine learning. Includes state-of-the-art generalized additive models in Explainable Boosting Machines for both regression and classification.
  • Functional Retrofitting is a scalable method to combine distributional and relational data.
  • drPCA is a framework for estimating principal components which differentiate sets of case/control samples.
  • GO_Translator is a set of simple utility functions for the Gene Ontology terms.