{ "_id": "6a1ae1ab1d7bb097a09edada", "Package": "Moonlight2R", "Type": "Package", "Title": "Identify oncogenes and tumor suppressor genes from omics data", "Version": "1.11.0", "Date": "", "Authors@R": "c(person(\"Mona\", \"Nourbakhsh\",\nrole=\"aut\"),\nperson(\"Astrid\", \"Saksager\",\nrole=\"aut\"),\nperson(\"Nikola\", \"Tom\",\nrole=\"aut\"),\nperson(\"Katrine\", \"Meldgård\",\nrole=\"aut\"),\nperson(\"Anna\", \"Melidi\",\nrole=\"aut\"),\nperson(\"Xi Steven\", \"Chen\",\nrole=\"aut\"),\nperson(\"Antonio\", \"Colaprico\",\nrole=\"aut\"),\nperson(\"Catharina\", \"Olsen\",\nrole=\"aut\"),\nperson(\"Alessia\", \"Campo\",\nrole=c(\"aut\")),\nperson(\"Matteo\", \"Tiberti\",\nrole=c(\"cre\", \"aut\"),\nemail=\"tiberti@cancer.dk\"),\nperson(\"Elena\", \"Papaleo\",\nrole=\"aut\",\n))", "Description": "The understanding of cancer mechanism requires the\nidentification of genes playing a role in the development of\nthe pathology and the characterization of their role (notably\noncogenes and tumor suppressors). We present an updated version\nof the R/bioconductor package called MoonlightR, namely\nMoonlight2R, which returns a list of candidate driver genes for\nspecific cancer types on the basis of omics data integration.\nThe Moonlight framework contains a primary layer where gene\nexpression data and information about biological processes are\nintegrated to predict genes called oncogenic mediators, divided\ninto putative tumor suppressors and putative oncogenes. This is\ndone through functional enrichment analyses, gene regulatory\nnetworks and upstream regulator analyses to score the\nimportance of well-known biological processes with respect to\nthe studied cancer type. By evaluating the effect of the\noncogenic mediators on biological processes or through random\nforests, the primary layer predicts two putative roles for the\noncogenic mediators: i) tumor suppressor genes (TSGs) and ii)\noncogenes (OCGs). As gene expression data alone is not enough\nto explain the deregulation of the genes, a second layer of\nevidence is needed. We have automated the integration of a\nsecondary mutational layer through new functionalities in\nMoonlight2R. These functionalities analyze mutations in the\ncancer cohort and classifies these into driver and passenger\nmutations using the driver mutation prediction tool,\nCScape-somatic. Those oncogenic mediators with at least one\ndriver mutation are retained as the driver genes. As a\nconsequence, this methodology does not only identify genes\nplaying a dual role (e.g. TSG in one cancer type and OCG in\nanother) but also helps in elucidating the biological processes\nunderlying their specific roles. In particular, Moonlight2R can\nbe used to discover OCGs and TSGs in the same cancer type. This\nmay for instance help in answering the question whether some\ngenes change role between early stages (I, II) and late stages\n(III, IV). In the future, this analysis could be useful to\ndetermine the causes of different resistances to\nchemotherapeutic treatments. An additional mechanistic layer\nevaluates if there are mutations affecting the protein\nstability of the transcription factors (TFs) of the TSGs and\nOCGs, as that may have an effect on the expression of the\ngenes.", "License": "GPL-3", "biocViews": "DNAMethylation, DifferentialMethylation, GeneRegulation,\nGeneExpression, MethylationArray, DifferentialExpression,\nPathways, Network, Survival, GeneSetEnrichment,\nNetworkEnrichment", "SystemRequirements": "CScapeSomatic", "VignetteBuilder": "knitr", "URL": "https://github.com/ELELAB/Moonlight2R", "BugReports": "https://github.com/ELELAB/Moonlight2R/issues", "RoxygenNote": "7.3.3", "LazyData": "false", "Encoding": "UTF-8", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev libglu1-mesa-dev make texlive\nlibbz2-dev libicu-dev libjpeg-dev liblzma-dev libpng-dev\nlibuv1-dev libxml2-dev libgl1-mesa-dev libssl-dev perl\nlibx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:01:32 UTC", "RemoteUrl": "https://github.com/bioc/Moonlight2R", "RemoteRef": "HEAD", "RemoteSha": "f947d16ced3766bab9e78fc0aac8a4a9e9137319", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:20:46 UTC", "User": "root" }, "Author": "Mona Nourbakhsh [aut],\nAstrid Saksager [aut],\nNikola Tom [aut],\nKatrine Meldgård [aut],\nAnna Melidi [aut],\nXi Steven Chen [aut],\nAntonio Colaprico [aut],\nCatharina Olsen [aut],\nAlessia Campo [aut],\nMatteo Tiberti [cre, aut],\nElena Papaleo [aut]", "Maintainer": "Matteo Tiberti ", "MD5sum": "48475b42235c91ef076cd3d3448eec33", "_user": "bioc", "_type": "src", "_file": "Moonlight2R_1.11.0.tar.gz", "_fileid": "2d44cde92bae5acff559d5e96e3a280555c94b51cd16259f039ec8dc6f27a465", "_filesize": 5374648, "_sha256": "2d44cde92bae5acff559d5e96e3a280555c94b51cd16259f039ec8dc6f27a465", "_created": "2026-05-30T09:20:46.000Z", "_published": "2026-05-30T13:10:03.507Z", "_jobs": [ { "job": 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