Package: DepInfeR
Type: Package
Title: Inferring tumor-specific cancer dependencies through integrating
        ex-vivo drug response assays and drug-protein profiling
Version: 1.14.0
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
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:15:57 UTC
RemoteUrl: https://github.com/bioc/DepInfeR
RemoteRef: RELEASE_3_22
RemoteSha: ce2b9fb7659a5ecc77d1c03a378b53c7ced639fd
NeedsCompilation: no
Packaged: 2025-11-11 13:57:39 UTC; root
Author: Junyan Lu [aut, cre] (ORCID: <https://orcid.org/0000-0002-9211-0746>),
  Alina Batzilla [aut]
Maintainer: Junyan Lu <jylu1118@gmail.com>
Built: R 4.5.2; ; 2025-11-11 14:03:13 UTC; windows
