DepInfeR

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

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.DepInfeR

Bioconductor version: Development (3.23)

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: https://doi.org/10.1101/2022.01.11.475864.

Author: Junyan Lu [aut, cre] ORCID iD ORCID: 0000-0002-9211-0746 , Alina Batzilla [aut]

Maintainer: Junyan Lu <jylu1118 at gmail.com>

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

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("DepInfeR")

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