mslp

This is the development version of mslp; for the stable release version, see mslp.

Predict synthetic lethal partners of tumour mutations

Bioconductor version: Development (3.21)

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>

Citation (from within R, enter citation("mslp")):

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

mslp	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Pharmacogenetics, Pharmacogenomics, Software
Version	1.9.0
In Bioconductor since	BioC 3.16 (R-4.2) (2 years)
License	GPL-3
Depends	R (>= 4.2.0)
Imports	data.table (>= 1.13.0), doRNG, fmsb, foreach, magrittr, org.Hs.eg.db, pROC, randomForest, RankProd, stats, utils
System Requirements
URL

Suggests	BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2, tinytest
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	mslp_1.9.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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