Package: DepInfeR
Type: Package
Title: Inferring tumor-specific cancer dependencies through integrating
        ex-vivo drug response assays and drug-protein profiling
Version: 1.15.0
Authors@R: 
  c(person(given = "Junyan",
           family = "Lu",
           role = c("aut", "cre"),
           email = "jylu1118@gmail.com",
           comment = c(ORCID = "0000-0002-9211-0746")),
    person(given = "Alina",
           family = "Batzilla",
           role = c("aut")))
Description: 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.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 4.2.0)
Imports: matrixStats, glmnet, stats, BiocParallel
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble,
        ggplot2, missForest, pheatmap, RColorBrewer, ggrepel,
        BiocStyle, ggbeeswarm
VignetteBuilder: knitr
RoxygenNote: 7.1.2
biocViews: Software, Regression, Pharmacogenetics, Pharmacogenomics,
        FunctionalGenomics
BugReports: https://github.com/Huber-group-EMBL/DepInfeR/issues
git_url: https://git.bioconductor.org/packages/DepInfeR
git_branch: devel
git_last_commit: b403931
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
Date/Publication: 2025-11-17
NeedsCompilation: no
Packaged: 2025-11-17 21:56:38 UTC; biocbuild
Author: Junyan Lu [aut, cre] (ORCID: <https://orcid.org/0000-0002-9211-0746>),
  Alina Batzilla [aut]
Maintainer: Junyan Lu <jylu1118@gmail.com>
Built: R 4.6.0; ; 2025-11-18 11:57:23 UTC; unix
