{ "_id": "6a493d5fa19c9318096e7599", "Package": "mslp", "Type": "Package", "Title": "Predict synthetic lethal partners of tumour mutations", "Version": "1.15.0", "Authors@R": "person(given = \"Chunxuan\", family = \"Shao\", role = c(\"aut\", \"cre\"), email = \"chunxuan@outlook.com\")", "Description": "An integrated pipeline to predict the potential synthetic\nlethality partners (SLPs) of tumour mutations, based on gene\nexpression, mutation profiling and cell line genetic screens\ndata. It has builtd-in support for data from cBioPortal. The\nprimary SLPs correlating with muations in WT and compensating\nfor the loss of function of mutations are predicted by random\nforest based methods (GENIE3) and Rank Products, respectively.\nGenetic screens are employed to identfy consensus SLPs leads to\nreduced cell viability when perturbed.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "false", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "biocViews": "Pharmacogenetics, Pharmacogenomics", "Config/pak/sysreqs": "libgmp3-dev libpng-dev libmpfr-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:37 UTC", "RemoteUrl": "https://github.com/bioc/mslp", "RemoteRef": "HEAD", "RemoteSha": "6b44cd84c33c4c8544cba99c3b51849d92693140", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 01:30:24 UTC", "User": "root" }, "Author": "Chunxuan Shao [aut, cre]", "Maintainer": "Chunxuan Shao ", "_user": "bioc", "_type": "src", "_file": "mslp_1.15.0.tar.gz", "_fileid": "https://r2.ropensci.org/06f28e0baaa69b7113692e72d3bc33a6a5fd3f727911ab0a8778a91f677286b3", "_filesize": 322435, "_sha256": "06f28e0baaa69b7113692e72d3bc33a6a5fd3f727911ab0a8778a91f677286b3", "_expires": "2026-10-12T17:05:33.000Z", "_created": "2026-07-04T01:30:24.000Z", "_published": "2026-07-04T17:05:35.186Z", "_bioccheck": { "error": 0, "warning": 0, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28690720217", "_status": "success", "_upstream": "https://github.com/bioc/mslp", "_commit": { "id": "6b44cd84c33c4c8544cba99c3b51849d92693140", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381117 }, "_maintainer": { "name": "Chunxuan Shao", "email": "chunxuan@outlook.com" }, "_distro": "resolute", "_jobs": [ { "job": 85150666946, "time": 178, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8077080185" }, { "job": 85150666813, "time": 259, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8077090537" }, { "job": 85150666941, "time": 211, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8077084464" }, { "job": 85150666906, "time": 116, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "8077072751" }, { "job": 85150666807, "time": 100, "config": "macos-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "8077070841" }, { "job": 85150666585, "time": 232, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8077059124" }, { "job": 85150666892, "time": 174, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8077079729" }, { "job": 85150666827, "time": 416, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8077113900" }, { "job": 85150666878, "time": 435, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8077116475" }, { "job": 85150666768, "time": 437, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8077116871" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "data.table", "version": ">= 1.13.0", "role": "Imports" }, { "package": "doRNG", "role": "Imports" }, { "package": "fmsb", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "org.Hs.eg.db", "role": "Imports" }, { "package": "pROC", "role": "Imports" }, { "package": "randomForest", "role": "Imports" }, { "package": "RankProd", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "doFuture", "role": "Suggests" }, { "package": "future", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "roxygen2", "role": "Suggests" }, { "package": "tinytest", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.15.0", "bioc": "3.24" }, { "branch": "release", "version": "1.14.0", "bioc": "3.23" } ], "_topics": [ "pharmacogenetics", "pharmacogenomics" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 1, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/mslp.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "comp_slp", "cons_slp", "corr_slp", "est_im", "genie3", "getlink", "merge_slp", "pp_tcga", "scr_slp" ], "_datasets": [ { "name": "example_comp_mut", "title": "Patients mutations to be use in the comp_slp", "object": "example_comp_mut", "file": "example_comp_mut.rda", "class": [ "data.table", "data.frame" ], "fields": [ "patientid", "mut_entrez" ], "rows": 138, "table": true, "tojson": true }, { "name": "example_compSLP", "title": "SLPs predicted by comp_slp", "object": "example_compSLP", "file": "example_compSLP.rda", "class": [ "data.table", "data.frame" ], "fields": [ "mut_entrez", "mut_symbol", "slp_entrez", "slp_symbol", "pvalue", "fdr" ], "rows": 61, "table": true, "tojson": true }, { "name": "example_corr_mut", "title": "Patients mutations to be use in the corr_slp", "object": "example_corr_mut", "file": "example_corr_mut.rda", "class": [ "data.table", "data.frame" ], "fields": [ "patientid", "mut_entrez" ], "rows": 114, "table": true, "tojson": true }, { "name": "example_corrSLP", "title": "SLPs predicted by corr_slp", "object": "example_corrSLP", "file": "example_corrSLP.rda", "class": [ "data.table", "data.frame" ], "fields": [ "mut_entrez", "mut_symbol", "slp_entrez", "slp_symbol", "im" ], "rows": 591, "table": true, "tojson": true }, { "name": "example_expr", "title": "Expression data to be used in comp_slp", "object": "example_expr", "file": "example_expr.rda", "class": [ "matrix", "array" ], "fields": [ "TCGA-BH-A0EE-01", "TCGA-AC-A5XS-01", "TCGA-AN-A0XW-01", "TCGA-E2-A1LI-01", "TCGA-B6-A0IQ-01", "TCGA-A7-A0CH-01", "TCGA-AO-A03M-01", "TCGA-A7-A5ZW-01", "TCGA-A8-A09V-01", "TCGA-EW-A1PG-01", "TCGA-GM-A5PV-01", "TCGA-D8-A73X-01", "TCGA-EW-A1IY-01", "TCGA-A8-A092-01", "TCGA-D8-A1XK-01", "TCGA-D8-A27V-01", "TCGA-AN-A0FY-01", "TCGA-A8-A06R-01", "TCGA-B6-A0I2-01", "TCGA-E2-A14N-01", "TCGA-LL-A7T0-01", "TCGA-C8-A137-01", "TCGA-E2-A109-01", "TCGA-A8-A07I-01", "TCGA-W8-A86G-01", "TCGA-BH-A0E1-01", "TCGA-BH-A1EO-01", "TCGA-D8-A1JM-01", "TCGA-AC-A5EH-01", "TCGA-A1-A0SJ-01", "TCGA-B6-A0IC-01", "TCGA-AN-A0XT-01", "TCGA-A2-A4RX-01", "TCGA-BH-A0BG-01", "TCGA-BH-A0HA-01", "TCGA-A1-A0SO-01", "TCGA-E2-A15J-01", "TCGA-E2-A14O-01", "TCGA-C8-A12P-01", "TCGA-BH-A0BJ-01", "TCGA-C8-A273-01" ], "rows": 290, "table": true, "tojson": true }, { "name": "example_z", "title": "Expression data to be used in corr_slp", "object": "example_z", "file": "example_z.rda", "class": [ "matrix", "array" ], "fields": [ "TCGA-BH-A0EE-01", "TCGA-AC-A5XS-01", "TCGA-AN-A0XW-01", "TCGA-E2-A1LI-01", "TCGA-B6-A0IQ-01", "TCGA-A7-A0CH-01", "TCGA-AO-A03M-01", "TCGA-A7-A5ZW-01", "TCGA-A8-A09V-01", "TCGA-EW-A1PG-01", "TCGA-GM-A5PV-01", "TCGA-D8-A73X-01", "TCGA-EW-A1IY-01", "TCGA-A8-A092-01", "TCGA-D8-A1XK-01", "TCGA-D8-A27V-01", "TCGA-AN-A0FY-01", "TCGA-A8-A06R-01", "TCGA-B6-A0I2-01", "TCGA-E2-A14N-01", "TCGA-LL-A7T0-01", "TCGA-C8-A137-01", "TCGA-E2-A109-01", "TCGA-A8-A07I-01", "TCGA-W8-A86G-01", "TCGA-BH-A0E1-01", "TCGA-BH-A1EO-01", "TCGA-D8-A1JM-01", "TCGA-AC-A5EH-01", "TCGA-A1-A0SJ-01", "TCGA-B6-A0IC-01", "TCGA-AN-A0XT-01", "TCGA-A2-A4RX-01", "TCGA-BH-A0BG-01", "TCGA-BH-A0HA-01", "TCGA-A1-A0SO-01", "TCGA-E2-A15J-01", "TCGA-E2-A14O-01", "TCGA-C8-A12P-01", "TCGA-BH-A0BJ-01", "TCGA-C8-A273-01" ], "rows": 290, "table": true, "tojson": true } ], "_help": [ { "page": "comp_slp", "title": "Identify SLPs via compensation", "topics": [ "comp_slp" ] }, { "page": "cons_slp", "title": "Identify consensus SLPs", "topics": [ "cons_slp" ] }, { "page": "corr_slp", "title": "Identify SLPs via correlation", "topics": [ "corr_slp" ] }, { "page": "est_im", "title": "Estimate the importance threshold for GENIE3", "topics": [ "est_im" ] }, { "page": "example_comp_mut", "title": "Patients mutations to be use in the comp_slp", "topics": [ "example_comp_mut" ] }, { "page": "example_compSLP", "title": "SLPs predicted by comp_slp", "topics": [ "example_compSLP" ] }, { "page": "example_corr_mut", "title": "Patients mutations to be use in the corr_slp", "topics": [ "example_corr_mut" ] }, { "page": "example_corrSLP", "title": "SLPs predicted by corr_slp", "topics": [ "example_corrSLP" ] }, { "page": "example_expr", "title": "Expression data to be used in comp_slp", "topics": [ "example_expr" ] }, { "page": "example_z", "title": "Expression data to be used in corr_slp", "topics": [ "example_z" ] }, { "page": "genie3", "title": "Run GENIE3", "topics": [ "genie3" ] }, { "page": "getlink", "title": "Get sorted list of regulatory links in GENIE3 results", "topics": [ "getlink" ] }, { "page": "merge_slp", "title": "Merge SLPs", "topics": [ "merge_slp" ] }, { "page": "pp_tcga", "title": "Process tumour genomic data", "topics": [ "pp_tcga" ] }, { "page": "scr_slp", "title": "Identify SLPs in screen hits", "topics": [ "scr_slp" ] } ], "_rundeps": [ "AnnotationDbi", "askpass", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "digest", "doRNG", "fastmap", "fmsb", "foreach", "generics", "glue", "gmp", "httr", "IRanges", "iterators", "jsonlite", "KEGGREST", "lifecycle", "magrittr", "memoise", "mime", "openssl", "org.Hs.eg.db", "pkgconfig", "png", "pROC", "R6", "randomForest", "RankProd", "Rcpp", "rlang", "Rmpfr", "rngtools", "RSQLite", "S4Vectors", "Seqinfo", "sys", "vctrs", "XVector" ], "_vignettes": [ { "source": "mslp.Rmd", "filename": "mslp.html", "title": "mslp", "author": "Chunxuan Shao", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Analysis", "Data preprocessing", "Call SLPs from compensationModule", "Call SLPs from correlationModule", "Call consensus SLPs", "Reference" ], "created": "2021-10-07 12:54:03", "modified": "2023-01-30 19:56:07", "commits": 12 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "mslp", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.15.0", "date": "2026-07-04T01:34:15.000Z", "distro": "resolute", "commit": "6b44cd84c33c4c8544cba99c3b51849d92693140", "fileid": "https://r2.ropensci.org/8d0d697759cb39d7aa4de8fb1a3b92114b1cf9530ac6ad3bedb731d652dd47c0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28690720217" }, { "r": "4.6.1", "os": "linux", "version": "1.15.0", "date": "2026-07-04T01:33:29.000Z", "distro": "resolute", "commit": "6b44cd84c33c4c8544cba99c3b51849d92693140", "fileid": "https://r2.ropensci.org/2b85fa5a85685079a2a3141267e0fadfa2165f89d39d806528f1623e7bc1746c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28690720217" }, { "r": "4.5.3", "os": "mac", "version": "1.15.0", "date": "2026-07-04T01:32:07.000Z", "commit": "6b44cd84c33c4c8544cba99c3b51849d92693140", "fileid": "https://r2.ropensci.org/058f267498d24a1bf888202df17502dca0e929d76a973546b4d7d0aa4f7b0a7e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28690720217" }, { "r": "4.6.1", "os": "mac", "version": "1.15.0", "date": "2026-07-04T01:31:51.000Z", "commit": "6b44cd84c33c4c8544cba99c3b51849d92693140", "fileid": "https://r2.ropensci.org/1dfe54e21d587b4319149bb6811e72621eb5016646139e1eef6cfb881ee14bc0", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28690720217" }, { "r": "4.6.0", "os": "wasm", "version": "1.15.0", "date": "2026-07-04T01:33:34.000Z", "commit": "6b44cd84c33c4c8544cba99c3b51849d92693140", "fileid": "https://r2.ropensci.org/c4f3cab18513a0d673f51bfa1d1ce94585b5dd496a3cc1c0fd2b8faee2ad09ce", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28690720217" }, { "r": "4.7.0", "os": "win", "version": "1.15.0", "date": "2026-07-04T01:36:45.000Z", "commit": "6b44cd84c33c4c8544cba99c3b51849d92693140", "fileid": "https://r2.ropensci.org/6821635ef1379f135e9ac2348fb25be1490a377d3d971d48c2f5efcd21c9a07f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28690720217" }, { "r": "4.5.3", "os": "win", "version": "1.15.0", "date": "2026-07-04T01:36:58.000Z", "commit": "6b44cd84c33c4c8544cba99c3b51849d92693140", "fileid": "https://r2.ropensci.org/da5653afddd58c5f6a5ceaeab9de61ab3d98ea997d52a3c6fb139f42156daa5a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28690720217" }, { "r": "4.6.1", "os": "win", "version": "1.15.0", "date": "2026-07-04T01:37:10.000Z", "commit": "6b44cd84c33c4c8544cba99c3b51849d92693140", "fileid": "https://r2.ropensci.org/dc4e202f23f4084e5fe74af3cf68457b3713fb1ef304abac367c32e69ac59689", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28690720217" } ] }