Huber-group-EMBL/DepInfeR: Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling

DepInfeR integrates two experimentally accessible input data matrices: the drug sensitivity profiles of cancer cell lines or primary tumors ex-vivo (X), and the drug affinities of a set of proteins (Y), to infer a matrix of molecular protein dependencies of the cancers (ß). DepInfeR deconvolutes the protein inhibition effect on the viability phenotype by using regularized multivariate linear regression. It assigns a “dependence coefficient” to each protein and each sample, and therefore could be used to gain a causal and accurate understanding of functional consequences of genomic aberrations in a heterogeneous disease, as well as to guide the choice of pharmacological intervention for a specific cancer type, sub-type, or an individual patient. For more information, please read out our paper: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010438

install.packages("remotes")
remotes::install_github("Huber-group-EMBL/DepInfeR")