Introduction | Installation | Analysis | Data preprocessing | Call SLPs from compensationModule | Call SLPs from correlationModule | Call consensus SLPs | Reference
Package: mslp 1.15.0
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:
mslp_1.15.0.tar.gz
mslp_1.15.0.zip(r-4.7)mslp_1.15.0.zip(r-4.6)mslp_1.15.0.zip(r-4.5)
mslp_1.15.0.tgz(r-4.6-any)mslp_1.15.0.tgz(r-4.5-any)
mslp_1.15.0.tar.gz(r-4.7-any)mslp_1.15.0.tar.gz(r-4.6-any)
mslp_1.15.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mslp/json (API)
| # Install 'mslp' in R: |
| install.packages('mslp', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- example_comp_mut - Patients mutations to be use in the comp_slp
- example_compSLP - SLPs predicted by comp_slp
- example_corr_mut - Patients mutations to be use in the corr_slp
- example_corrSLP - SLPs predicted by corr_slp
- example_expr - Expression data to be used in comp_slp
- example_z - Expression data to be used in corr_slp
On BioConductor:mslp-1.15.0(bioc 3.24)mslp-1.14.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
pharmacogeneticspharmacogenomics
Last updated from:6b44cd84c3. Checks:1 NOTE, 7 OK, 2 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 178 | ||
| linux-devel-x86_64 | OK | 259 | ||
| source / vignettes | OK | 232 | ||
| linux-release-x86_64 | OK | 211 | ||
| macos-release-arm64 | ERROR | 100 | ||
| macos-oldrel-arm64 | ERROR | 116 | ||
| windows-devel | OK | 416 | ||
| windows-release | OK | 437 | ||
| windows-oldrel | OK | 435 | ||
| wasm-release | OK | 174 |
Exports:comp_slpcons_slpcorr_slpest_imgenie3getlinkmerge_slppp_tcgascr_slp
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicodetoolscpp11crayoncurldata.tableDBIdigestdoRNGfastmapfmsbforeachgenericsgluegmphttrIRangesiteratorsjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslorg.Hs.eg.dbpkgconfigpngpROCR6randomForestRankProdRcpprlangRmpfrrngtoolsRSQLiteS4VectorsSeqinfosysvctrsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Identify SLPs via compensation | comp_slp |
| Identify consensus SLPs | cons_slp |
| Identify SLPs via correlation | corr_slp |
| Estimate the importance threshold for GENIE3 | est_im |
| Patients mutations to be use in the comp_slp | example_comp_mut |
| SLPs predicted by comp_slp | example_compSLP |
| Patients mutations to be use in the corr_slp | example_corr_mut |
| SLPs predicted by corr_slp | example_corrSLP |
| Expression data to be used in comp_slp | example_expr |
| Expression data to be used in corr_slp | example_z |
| Run GENIE3 | genie3 |
| Get sorted list of regulatory links in GENIE3 results | getlink |
| Merge SLPs | merge_slp |
| Process tumour genomic data | pp_tcga |
| Identify SLPs in screen hits | scr_slp |