recipe bioconductor-depinfer

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

Homepage:

https://bioconductor.org/packages/3.20/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:

1.14.0-0,  1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-0

Depends:

• on bioconductor-biocparallel >=1.44.0,<1.45.0

• on r-base >=4.5,<4.6.0a0

• on r-glmnet

• on r-matrixstats

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-depinfer

to add into an existing workspace instead, run:

pixi add bioconductor-depinfer

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-depinfer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-depinfer

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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