recipe bioconductor-depinfer

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

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/DepInfeR.html

License:

GPL-3

Recipe:

/bioconductor-depinfer/meta.yaml

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.

package bioconductor-depinfer

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends r-base:

>=4.3,<4.4.0a0

depends r-glmnet:

depends r-matrixstats:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-depinfer

and update with::

   mamba update bioconductor-depinfer

To create a new environment, run:

mamba create --name myenvname bioconductor-depinfer

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-depinfer:<tag>

(see `bioconductor-depinfer/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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