DepInfeR

DOI: 10.18129/B9.bioc.DepInfeR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see DepInfeR.

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

Bioconductor version: 3.16

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] , Alina Batzilla [aut]

Maintainer: Junyan Lu <jylu1118 at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DepInfeR")

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

Documentation

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

browseVignettes("DepInfeR")

 

HTML	R Script	DepInfeR
PDF		Reference Manual
Text		NEWS

Details

biocViews	FunctionalGenomics, Pharmacogenetics, Pharmacogenomics, Regression, Software
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	GPL-3
Depends	R (>= 4.2.0)
Imports	matrixStats, glmnet, stats, BiocParallel
LinkingTo
Suggests	testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble, ggplot2, missForest, pheatmap, RColorBrewer, ggrepel, ggbeeswarm
SystemRequirements
Enhances
URL
BugReports	https://github.com/Huber-group-EMBL/DepInfeR/issues
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_1.2.0.tar.gz
Windows Binary	DepInfeR_1.2.0.zip
macOS Binary (x86_64)	DepInfeR_1.2.0.tgz
macOS Binary (arm64)	DepInfeR_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DepInfeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DepInfeR
Bioc Package Browser	https://code.bioconductor.org/browse/DepInfeR/
Package Short Url	https://bioconductor.org/packages/DepInfeR/
Package Downloads Report	Download Stats