Package: DepInfeR 1.9.0

Junyan Lu

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

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.

Authors:Junyan Lu [aut, cre], Alina Batzilla [aut]

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Bug tracker:https://github.com/huber-group-embl/depinfer/issues

On BioConductor:DepInfeR-1.9.0(bioc 3.20)DepInfeR-1.8.0(bioc 3.19)

bioconductor-package

2 exports 0.49 score 19 dependencies

Last updated 2 months agofrom:7349c4860f

Exports:processTargetrunLASSORegression

Dependencies:BHBiocParallelcodetoolscpp11foreachformatRfutile.loggerfutile.optionsglmnetiteratorslambda.rlatticeMatrixmatrixStatsRcppRcppEigenshapesnowsurvival