DOI: 10.18129/B9.bioc.mslp  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see mslp.

Predict synthetic lethal partners of tumour mutations

Bioconductor version: 3.16

An integrated pipeline to predict the potential synthetic lethality partners (SLPs) of tumour mutations, based on gene expression, mutation profiling and cell line genetic screens data. It has builtd-in support for data from cBioPortal. The primary SLPs correlating with muations in WT and compensating for the loss of function of mutations are predicted by random forest based methods (GENIE3) and Rank Products, respectively. Genetic screens are employed to identfy consensus SLPs leads to reduced cell viability when perturbed.

Author: Chunxuan Shao [aut, cre]

Maintainer: Chunxuan Shao <chunxuan at>

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biocViews Pharmacogenetics, Pharmacogenomics, Software
Version 1.0.2
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License GPL-3
Depends R (>= 4.2.0), data.table (>= 1.13.0)
Imports doRNG, fmsb, foreach, magrittr,, pROC, randomForest, RankProd, stats, utils
Suggests BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2, tinytest
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