DepInfeR
This is the released version of DepInfeR; for the devel version, see DepInfeR.
Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling
Bioconductor version: Release (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]
, Alina Batzilla [aut]
Maintainer: Junyan Lu <jylu1118 at gmail.com>
citation("DepInfeR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| DepInfeR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FunctionalGenomics, Pharmacogenetics, Pharmacogenomics, Regression, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4.5 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_1.16.0.tar.gz |
| Windows Binary (x86_64) | DepInfeR_1.16.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | DepInfeR_1.16.0.tgz |
| macOS Binary (sonoma-arm64) | DepInfeR_1.16.0.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 |