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
Bioconductor version: Development (3.21)
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:
Maintainer: Junyan Lu <jylu1118 at gmail.com>
citation("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.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DepInfeR")| DepInfeR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FunctionalGenomics, Pharmacogenetics, Pharmacogenomics, Regression, Software |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0) |
| Imports | matrixStats, glmnet, stats, BiocParallel |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/Huber-group-EMBL/DepInfeR/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble, ggplot2, missForest, pheatmap, RColorBrewer, ggrepel, BiocStyle, ggbeeswarm |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DepInfeR_1.11.0.tar.gz |
| Windows Binary (x86_64) | DepInfeR_1.11.0.zip |
| macOS Binary (x86_64) | DepInfeR_1.11.0.tgz |
| macOS Binary (arm64) | DepInfeR_1.11.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DepInfeR |
| Source Repository (Developer Access) | git clone [email protected]:packages/DepInfeR |
| Bioc Package Browser | https://code.bioconductor.org/browse/DepInfeR/ |
| Package Short Url | https://bioconductor.org/packages/DepInfeR/ |
| Package Downloads Report | Download Stats |