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11, "table": true, "tojson": true }, { "name": "depMapXPR_subset", "title": "Example gene expression input matrix", "object": "depMapXPR_subset", "class": [ "data.frame" ], "fields": [ "NIHOVCAR3", "HL60", "CACO2", "HEL", "HEL9217", "MONOMAC6", "LS513", "A101D", "C2BBE1", "NCIH2077", "253J", "HCC827", "ONCODG1", "HS294T", "NCIH1581", "SLR21", "SKBR3", "T24", "MCF7", "MHHCALL2", "NCIH1693", "PATU8988S", "PATU8988T", "OPM2", "CH157MN", "253JBV", "GOS3", "KPL1", "HCC827GR5", "PC14", "PANC0213", "MHHCALL3", "NCIH1819", "PLB985", "NCIH1650", "U343", "S117", "EHEB", "SKNMC", "U118MG", "RDES", "PANC0203", "HS895T", "MDAMB134VI", "MV411", "ACHN", "GCIY", "TOV112D", "HEKTE", "NCIH929", "TE617T", "A673", "KARPAS299", "HT1080", "D283MED", "DOHH2", "OPM1", "ML1", "SUPB15", "PANC1005", "HH", "RERFLCMS", "HS616T", "SALE", "OCIAML5", "HCC4006", "HS683", "REC1", "HS611T", "697", "HS706T", "MEG01", "GRANTA519", "KU812", "U87MG", "NCO2", "MJ", "MHHNB11", "TE125T", "BDCM", "GDM1", "G292CLONEA141B1", 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Introduction", "Citing MultiSEp", "2. Quickstart", "Predicting Synthetic Lethality (SL) and other gene dependencies with mts_omics()", "Predicting SL with CRISPR and gene expression (SynLeGG)", "Induced dependency prediction with CRISPR and gene expression (SynLeGG)", "Predicting SL with mutation and gene expression (SynLeGG)", "3. Prediction of Gene Dependency Relationships (GDRs) with Functional Genomics Data", "Data partitioning to map gene function states", "Unsupervised clustering to reveal gene states for continuous data", "Threshold-based partitioning of continuous data", "Partitioning categorical data", "Analysing canonical dependency patterns for gene pairs", "Mapping GDRs with sample enrichment: CRISPR data", "Tissue-specific GDR detection", "Predicting tissue-specific GDRs with transcriptome data", "Predicting tissue-specific GDRs with transcriptome and CRISPR data", "Tissue-specific GDR detection (SynLeGG)", "Induced dependency prediction (t-test)", "Mutation and expression GDRs (SynLeGG)", "Analysis of mutational neighbourhoods in SL networks for therapeutic target prioritisation", "4. Running MultiSEp in a High-Performance Computing (HPC) Environment for Evaluation of Context-specific SL at Genome Scale", "Step 1: Produce gene expression clusters", "Step 2: Preparing the clustered genes for parallel processing", "Step 3: Predicting SL with mts_omics()", "Step 4: Identifying deleterious mutations to inform drug discovery", "Step 5: Predicting the population coverage achieved by inhibition of a candidate target gene", "Visualisation of predicted SL network for Multiple Myeloma", "5. References" ], "created": "2026-08-27 10:30:02", "modified": "2026-08-27 10:30:02", "commits": 1 } ], "_score": 2, "_indexed": true, "_nocasepkg": "multisep", "_universes": [ "ianoverton" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "4.1.3", "date": "2026-09-26T09:55:28.000Z", "distro": "resolute", "commit": "704d059e704b80de65a6c6d1125c2e48a0c284e9", "fileid": "https://r2.ropensci.org/6562c164b549721353d4eb9244d15843c6b5139d04420f9cad8f01ba539ed75a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ianoverton/actions/runs/36233876592" }, { "r": "4.6.1", "os": "linux", "version": "4.1.3", "date": "2026-09-26T09:55:25.000Z", "distro": "resolute", "commit": "704d059e704b80de65a6c6d1125c2e48a0c284e9", "fileid": "https://r2.ropensci.org/56e45255598ef34e0e979cec460f361b86b16829e2aae5c4cca31352088398e4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ianoverton/actions/runs/36233876592" }, { "r": "4.5.3", "os": "mac", "version": "4.1.3", "date": "2026-09-26T09:55:12.000Z", "commit": "704d059e704b80de65a6c6d1125c2e48a0c284e9", "fileid": "https://r2.ropensci.org/d632334aee45303eee07fde86fabd9436c77b34ae6094cf1468010538b714001", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ianoverton/actions/runs/36233876592" }, { "r": "4.6.1", "os": "mac", "version": "4.1.3", "date": "2026-09-26T09:55:27.000Z", "commit": "704d059e704b80de65a6c6d1125c2e48a0c284e9", "fileid": "https://r2.ropensci.org/d26a7829dfe2fd208fd7eb99d5c0726c117fc9181b64f2928c43e5126d38ced4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ianoverton/actions/runs/36233876592" }, { "r": "4.6.0", "os": "wasm", "version": "4.1.3", "date": "2026-09-26T09:55:29.000Z", "commit": "704d059e704b80de65a6c6d1125c2e48a0c284e9", "fileid": "https://r2.ropensci.org/02ef507ff7864a3b8c7d51737e0f30dfc21e05fee893ccb636471d761c2b720a", "status": "success", "buildurl": "https://github.com/r-universe/ianoverton/actions/runs/36233876592" }, { "r": "4.7.0", "os": "win", "version": "4.1.3", "date": "2026-09-26T09:54:13.000Z", "commit": "704d059e704b80de65a6c6d1125c2e48a0c284e9", "fileid": "https://r2.ropensci.org/e7032998f419fad773e14b990091ce47f0e814d8260b8acf9eaea7c0ada53842", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ianoverton/actions/runs/36233876592" }, { "r": "4.5.3", "os": "win", "version": "4.1.3", "date": "2026-09-26T09:54:16.000Z", "commit": "704d059e704b80de65a6c6d1125c2e48a0c284e9", "fileid": "https://r2.ropensci.org/72ea78a8576506df3fdc7bd84f543a80c8ce55d46e72c3a2fe1a957032206452", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ianoverton/actions/runs/36233876592" }, { "r": "4.6.1", "os": "win", "version": "4.1.3", "date": "2026-09-26T09:54:19.000Z", "commit": "704d059e704b80de65a6c6d1125c2e48a0c284e9", "fileid": "https://r2.ropensci.org/aba3f1b33c09754a0d46e6184bd77d558ce8339a65414e13aec6044941918e3c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/ianoverton/actions/runs/36233876592" } ] }