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This is the development version of DepInfeR; for the stable release version, see DepInfeR.

Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling

Bioconductor version: Development (3.20)

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 preprint on bioRxiv:

Author: Junyan Lu [aut, cre] , Alina Batzilla [aut]

Maintainer: Junyan Lu <jylu1118 at>

Citation (from within R, enter citation("DepInfeR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

DepInfeR HTML R Script
Reference Manual PDF


biocViews FunctionalGenomics, Pharmacogenetics, Pharmacogenomics, Regression, Software
Version 1.9.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.2.0)
Imports matrixStats, glmnet, stats, BiocParallel
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Suggests testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble, ggplot2, missForest, pheatmap, RColorBrewer, ggrepel, BiocStyle, ggbeeswarm
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Source Package DepInfeR_1.9.0.tar.gz
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