Our Resources

Software

• TRANSACT
  Clinical drug response prediction from cell line screens, using non- linear alignment of tumor and cell line gene expression profiles.
  Publication
  Python Package
  
  
• PRECISE
  Linear alignment of gene expression profiles by systematic comparison of principal components.
  Publication
  Python Package
  
  
• WON-PARAFAC
  Weighted orthogonal non-negative (WON) parallel factor analysis (PARAFAC)
  Publication
  Matlab code
  
  
• FlexGSEA
  Performs gene-set enrichment analysis with sample permutation. Very flexible, including support for RNAseq data.
  R Package
  
  
• MixedIC50
  A mixed model approach to IC50 estimation that enables simultaneous estimation of IC50 values across the entire set of cell lines and compounds. We show that this approach improves the accuracy of the estimates and significantly reduces the compute time.
  Publication
  R Package
  
  
• TANDEM
  A two-stage penalized linear regression approach that uses upstream (genomics) and downstream (transcriptomics) to predict drug response. It results in models that are more interpretable while maintaining similar predictive performance.
  Publication
  R Package can be installed from CRAN install.packages("TANDEM")
  
  
• DISCOVER
  Identifies co-occurrence and mutual exclusivity in somatic mutations using an elegant analytical null-model, which we show to faithfully recapitulate the nominal rates. The method suggests that many of the reported co-occurrences are in fact expected based on chance alone.
  Publication
  R and Python Packages
  
  
• OncoScape
  Prioritizes oncogenes and tumor suppressor genes based on the integration of various molecular data types.
  Publication
  TCGA pan-cancer results
  Code
  
  
• RUBIC
  Pinpoint driver genes in focal recurrent aberrations (across tumor samples) in DNA somatic copy number data.
  Publication
  R Package
  
  
• BCM
  A software package with samplers for Bayesian inference of computational models
  Publication
  Code and Documentation
  
  
• Mvdens
  R package for multivariate posterior distribution approximation from Monte Carlo samples.
  Publication
  R Package

See also our Github page: https://github.com/NKI-CCB