Package: mslp 1.9.0

Chunxuan Shao

mslp: Predict synthetic lethal partners of tumour mutations

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.

Authors:Chunxuan Shao [aut, cre]

mslp_1.9.0.tar.gz
mslp_1.9.0.zip(r-4.5)mslp_1.9.0.zip(r-4.4)mslp_1.9.0.zip(r-4.3)
mslp_1.9.0.tgz(r-4.5-any)mslp_1.9.0.tgz(r-4.4-any)mslp_1.9.0.tgz(r-4.3-any)
mslp_1.9.0.tar.gz(r-4.5-noble)mslp_1.9.0.tar.gz(r-4.4-noble)
mslp_1.9.0.tgz(r-4.4-emscripten)mslp_1.9.0.tgz(r-4.3-emscripten)
mslp.pdf |mslp.html
mslp/json (API)
NEWS

# Install 'mslp' in R:
install.packages('mslp', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:mslp-1.9.0(bioc 3.21)mslp-1.8.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

pharmacogeneticspharmacogenomics

3.30 score 1 scripts 202 downloads 9 exports 55 dependencies

Last updated 5 months agofrom:ee73d2b23e. Checks:6 OK, 3 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 29 2025
R-4.5-winOKMar 29 2025
R-4.5-macERRORMar 29 2025
R-4.5-linuxOKMar 29 2025
R-4.4-winOKMar 29 2025
R-4.4-macERRORMar 29 2025
R-4.4-linuxOKMar 29 2025
R-4.3-winOKMar 29 2025
R-4.3-macERRORMar 29 2025

Exports:comp_slpcons_slpcorr_slpest_imgenie3getlinkmerge_slppp_tcgascr_slp

Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurldata.tableDBIdigestdoRNGfastmapfmsbforeachgenericsGenomeInfoDbGenomeInfoDbDatagluegmphttrIRangesiteratorsjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslorg.Hs.eg.dbpkgconfigplogrplyrpngpROCR6randomForestRankProdRcpprlangRmpfrrngtoolsRSQLiteS4VectorssysUCSC.utilsvctrsXVector

mslp

Rendered frommslp.Rmdusingknitr::rmarkdownon Mar 29 2025.

Last update: 2023-01-30
Started: 2021-10-07