{ "_id": "6a1ac4161d7bb097a09dafb2", "Package": "MoonlightR", "Type": "Package", "Title": "Identify oncogenes and tumor suppressor genes from omics data", "Version": "1.39.0", "Date": "07-08-2020", "Authors@R": "c(person(\"Antonio\", \"Colaprico\",\nrole=\"aut\"),\nperson(\"Catharina\", \"Olsen\",\nrole=\"aut\"),\nperson(\"Matthew H.\", \"Bailey\",\nrole=\"aut\"),\nperson(\"Gabriel J.\", \"Odom\",\nrole=\"aut\"),\nperson(\"Thilde\", \"Terkelsen\",\nrole=\"aut\"),\nperson(\"Mona\", \"Nourbakhsh\",\nrole=\"aut\"),\nperson(\"Astrid\", \"Saksager\",\nrole=\"aut\"),\nperson(\"Tiago C.\", \"Silva\",\nrole=\"aut\"),\nperson(\"André V.\", \"Olsen\",\nrole=\"aut\"),\nperson(\"Laura\", \"Cantini\",\nrole=\"aut\"),\nperson(\"Andrei\", \"Zinovyev\",\nrole=\"aut\"),\nperson(\"Emmanuel\", \"Barillot\",\nrole=\"aut\"),\nperson(\"Houtan\", \"Noushmehr\",\nrole=\"aut\"),\nperson(\"Gloria\", \"Bertoli\",\nrole=\"aut\"),\nperson(\"Isabella\", \"Castiglioni\",\nrole=\"aut\"),\nperson(\"Claudia\",\"Cava\",\nrole=\"aut\"),\nperson(\"Gianluca\", \"Bontempi\",\nrole=\"aut\"),\nperson(\"Xi Steven\", \"Chen\",\nrole=\"aut\"),\nperson(\"Elena\", \"Papaleo\",\nrole=\"aut\"),\nperson(\"Matteo\", \"Tiberti\",\nrole=c(\"cre\", \"aut\"),\nemail=\"tiberti@cancer.dk\",\n))", "Description": "Motivation: The understanding of cancer mechanism requires\nthe identification of genes playing a role in the development\nof the pathology and the characterization of their role\n(notably oncogenes and tumor suppressors). Results: We present\nan R/bioconductor package called MoonlightR which returns a\nlist of candidate driver genes for specific cancer types on the\nbasis of TCGA expression data. The method first infers gene\nregulatory networks and then carries out a functional\nenrichment analysis (FEA) (implementing an upstream regulator\nanalysis, URA) to score the importance of well-known biological\nprocesses with respect to the studied cancer type. Eventually,\nby means of random forests, MoonlightR predicts two specific\nroles for the candidate driver genes: i) tumor suppressor genes\n(TSGs) and ii) oncogenes (OCGs). As a consequence, this\nmethodology does not only identify genes playing a dual role\n(e.g. TSG in one cancer type and OCG in another) but also helps\nin elucidating the biological processes underlying their\nspecific roles. In particular, MoonlightR can be used to\ndiscover OCGs and TSGs in the same cancer type. This may help\nin answering the question whether some genes change role\nbetween early stages (I, II) and late stages (III, IV) in\nbreast cancer. In the future, this analysis could be useful to\ndetermine the causes of different resistances to\nchemotherapeutic treatments.", "License": "GPL (>= 3)", "biocViews": "DNAMethylation, DifferentialMethylation, GeneRegulation,\nGeneExpression, MethylationArray, DifferentialExpression,\nPathways, Network, Survival, GeneSetEnrichment,\nNetworkEnrichment", "VignetteBuilder": "knitr", "LazyData": "true", "URL": "https://github.com/ELELAB/MoonlightR", "BugReports": "https://github.com/ELELAB/MoonlightR/issues", "RoxygenNote": "7.2.3", "Encoding": "UTF-8", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev libglu1-mesa-dev make texlive\nlibicu-dev libjpeg-dev libpng-dev libuv1-dev libxml2-dev\nlibgl1-mesa-dev libssl-dev libx11-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:44:28 UTC", "RemoteUrl": "https://github.com/bioc/MoonlightR", "RemoteRef": "HEAD", "RemoteSha": "b7cfad849539c019ba1e2b8ded50f1b510171488", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:40:30 UTC", "User": "root" }, "Author": "Antonio Colaprico [aut],\nCatharina Olsen [aut],\nMatthew H. Bailey [aut],\nGabriel J. Odom [aut],\nThilde Terkelsen [aut],\nMona Nourbakhsh [aut],\nAstrid Saksager [aut],\nTiago C. Silva [aut],\nAndré V. Olsen [aut],\nLaura Cantini [aut],\nAndrei Zinovyev [aut],\nEmmanuel Barillot [aut],\nHoutan Noushmehr [aut],\nGloria Bertoli [aut],\nIsabella Castiglioni [aut],\nClaudia Cava [aut],\nGianluca Bontempi [aut],\nXi Steven Chen [aut],\nElena Papaleo [aut],\nMatteo Tiberti [cre, aut]", "Maintainer": "Matteo Tiberti ", "MD5sum": "4f248cf259a8ae4e4b49bceac78c37c9", "_user": "bioc", "_type": "src", "_file": "MoonlightR_1.39.0.tar.gz", "_fileid": "9ed4c58004dd5f73fbcb94d72634f3681bb1df8c42af28e8469fe525b4baccde", "_filesize": 15509464, "_sha256": "9ed4c58004dd5f73fbcb94d72634f3681bb1df8c42af28e8469fe525b4baccde", "_created": "2026-05-30T07:40:30.000Z", "_published": "2026-05-30T11:03:50.824Z", "_jobs": [ { "job": 78634232748, "time": 304, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306584379" }, { "job": 78634232759, "time": 603, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306613467" }, { "job": 78634232756, "time": 634, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306616479" }, { "job": 78634232757, "time": 327, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307714966" }, { "job": 78634232754, "time": 249, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307707923" }, { "job": 78633834493, "time": 465, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306554381" }, { "job": 78634232751, "time": 242, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306578462" }, { "job": 78634232780, "time": 346, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306588327" }, { "job": 78634232758, "time": 351, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306589010" }, { "job": 78634232761, "time": 433, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306596939" } ], "_bioccheck": { "error": 2, "warning": 2, "note": 18 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678187114", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/MoonlightR", "_commit": { "id": "b7cfad849539c019ba1e2b8ded50f1b510171488", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380268 }, "_maintainer": { "name": "Matteo Tiberti", "email": "tiberti@cancer.dk", "login": "mtiberti-btf", "description": "", "uuid": 112105347 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "doParallel", "role": "Depends" }, { "package": "foreach", "role": "Depends" }, { "package": "parmigene", "role": "Imports" }, { "package": "randomForest", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "circlize", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "HiveR", "role": "Imports" }, { "package": "clusterProfiler", "role": "Imports" }, { "package": "DOSE", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "TCGAbiolinks", "role": "Imports" }, { "package": "GEOquery", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "RISmed", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "roxygen2", "role": "Suggests" }, { "package": "png", "role": "Suggests" }, { "package": "edgeR", "role": "Suggests" } 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"page": "FEA", "title": "FEA", "topics": [ "FEA" ] }, { "page": "GDCprojects", "title": "Information on GDC projects", "topics": [ "GDCprojects" ] }, { "page": "geneInfo", "title": "Information about genes for normalization", "topics": [ "geneInfo" ] }, { "page": "GEO_TCGAtab", "title": "Information on GEO data (and overlap with TCGA)#' A data set containing the following data:", "topics": [ "GEO_TCGAtab" ] }, { "page": "getDataGEO", "title": "getDataGEO", "topics": [ "getDataGEO" ] }, { "page": "getDataTCGA", "title": "getDataTCGA", "topics": [ "getDataTCGA" ] }, { "page": "GRN", "title": "Generate network", "topics": [ "GRN" ] }, { "page": "GSEA", "title": "GSEA", "topics": [ "GSEA" ] }, { "page": "knownDriverGenes", "title": "Information on known cancer driver gene from COSMIC", "topics": [ "knownDriverGenes" ] }, { "page": "listMoonlight", "title": "Output list from Moonlight", "topics": [ "listMoonlight" ] }, { "page": "LPA", "title": "LPA", "topics": [ "LPA" ] }, { "page": "moonlight", "title": "moonlight pipeline", "topics": [ "moonlight" ] }, { "page": "MoonlightR", "title": "MoonlightR", "topics": [ "MoonlightR" ] }, { "page": "plotCircos", "title": "plotCircos", "topics": [ "plotCircos" ] }, { "page": "plotFEA", "title": "plotFEA", "topics": [ "plotFEA" ] }, { "page": "plotNetworkHive", "title": "plotNetworkHive: Hive network plot", "topics": [ "plotNetworkHive" ] }, { "page": "plotURA", "title": "plotURA: Upstream regulatory analysis heatmap plot", "topics": [ "plotURA" ] }, { "page": "PRA", "title": "Pattern Recognition Analysis (PRA)", "topics": [ "PRA" ] }, { "page": "tabGrowBlock", "title": "Information growing/blocking characteristics for 101 selected biological processes", "topics": [ "tabGrowBlock" ] }, { "page": "URA", "title": "URA Upstream Regulator Analysis", "topics": [ "URA" ] } ], "_readme": "https://github.com/bioc/MoonlightR/raw/HEAD/README.md", "_rundeps": [ "abind", "aisdk", "AnnotationDbi", "ape", "aplot", "askpass", "base64enc", 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multiple role of biomarkers as oncogene or tumorsuppressor in different tumor types and stages.", "author": "Antonio Colaprico^+^ , Catharina Olsen^+^, Claudia Cava, Thilde Terkelsen, Laura Cantini, Gloria Bertoli, Andre Olsen, Andrei Zinovyev, Emmanuel Barillot, Isabella Castiglioni, Elena Papaleo, Gianluca Bontempi", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "Introduction", "Moonlight's pipeline", "Moonlight's proposed workflow", "Installation", "Citation", "Download: Get TCGA data", "getDataTCGA: Search by cancer type and data type [Gene Expression]", "getDataTCGA: Search by cancer type and data type [Methylation]", "Download: Get GEO data", "getDataGEO: Search by cancer type and data type [Gene Expression]", "Analysis: To analyze TCGA data", "DPA: Differential Phenotype Analysis", "FEA: Functional Enrichment Analysis", "FEAplot: Functional Enrichment Analysis Plot", "GRN: Gene Regulatory Network", "URA: Upstream Regulator Analysis", "PRA: Pattern Regognition Analysis", "plotNetworkHive: GRN hive visualization taking into account Cosmic cancer genes", "TCGA Downstream Analysis: Case Studies", "Case study n. 1: Downstream analysis LUAD", "plotURA: Upstream regulatory analysis plot", "Case study n. 2: Expression pipeline Pan Cancer 5 cancer types", "plotCircos: Moonlight Circos Plot", "Case study n. 3: Downstream analysis BRCA with stages", "References" ], "created": "2016-09-24 15:39:18", "modified": "2022-10-11 08:23:03", "commits": 15 } ], "_score": 6.572871602200481, "_indexed": true, "_nocasepkg": "moonlightr", "_universes": [ "bioc", "mtiberti-btf", "elelab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.39.0", "date": "2026-05-30T07:45:49.000Z", "distro": "noble", "commit": "b7cfad849539c019ba1e2b8ded50f1b510171488", "fileid": "bd3084d031e3721f9a67fb286849f76fe2c3e199fa989e001fffd62f0d97f57d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678187114" }, { "r": 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