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 profilingBioconductor version: Development (3.22)
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 (Ã). DepInfeR deconvolutes the protein inhibition effect on the viability phenotype by using regularized multivariate linear regression. It assigns a âdependence coefficientâ 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: 0000-0002-9211-0746 , Alina Batzilla [aut]
Maintainer: Junyan Lu <jylu1118 at gmail.com>
Citation (from within R, entercitation("DepInfeR")): Installation
To install this package, start R (version "4.5") 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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DepInfeR")Follow Installation instructions to use this package in your R session.
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