mslp
Predict synthetic lethal partners of tumour mutations
Bioconductor version: Release (3.19)
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("mslp")):
Installation
To install this package, start R (version "4.4") 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")| mslp | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Pharmacogenetics, Pharmacogenomics, Software |
| Version | 1.6.0 |
| 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 |
See More
| Suggests | BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2, tinytest |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | mslp_1.6.0.tar.gz |
| Windows Binary (x86_64) | mslp_1.6.0.zip |
| macOS Binary (x86_64) | mslp_1.6.0.tgz |
| 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 |