mslp

DOI: 10.18129/B9.bioc.mslp  

Predict synthetic lethal partners of tumour mutations

Bioconductor version: Release (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 outlook.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("mslp")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("mslp")

 

HTML	R Script	mslp
PDF		Reference Manual
Text		NEWS

Details

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, org.Hs.eg.db, pROC, randomForest, RankProd, stats, utils
LinkingTo
Suggests	BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2, tinytest
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	mslp_1.0.2.tar.gz
Windows Binary	mslp_1.0.2.zip
macOS Binary (x86_64)	mslp_1.0.2.tgz
macOS Binary (arm64)	mslp_1.0.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mslp
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mslp
Bioc Package Browser	https://code.bioconductor.org/browse/mslp/
Package Short Url	https://bioconductor.org/packages/mslp/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive