DOI: 10.18129/B9.bioc.DepInfeR  

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

Bioconductor version: Release (3.17)

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 "4.3") and enter:

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


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:



HTML R Script DepInfeR
PDF   Reference Manual
Text   NEWS


biocViews FunctionalGenomics, Pharmacogenetics, Pharmacogenomics, Regression, Software
Version 1.4.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License GPL-3
Depends R (>= 4.2.0)
Imports matrixStats, glmnet, stats, BiocParallel
Suggests testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble, ggplot2, missForest, pheatmap, RColorBrewer, ggrepel, BiocStyle, ggbeeswarm
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DepInfeR_1.4.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) DepInfeR_1.4.0.tgz
macOS Binary (arm64) DepInfeR_1.4.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: