{ "_id": "6a102971acfb0bcc41c915b6", "Package": "AMARETTO", "Type": "Package", "Title": "Regulatory Network Inference and Driver Gene Evaluation using\nIntegrative Multi-Omics Analysis and Penalized Regression", "Version": "1.29.0", "Date": "2016-06-06", "Author": "Jayendra Shinde, Celine Everaert, Shaimaa Bakr, Mohsen Nabian,\nJishu Xu, Vincent Carey, Nathalie Pochet and Olivier Gevaert", "Maintainer": "Olivier Gevaert ", "Description": "Integrating an increasing number of available multi-omics\ncancer data remains one of the main challenges to improve our\nunderstanding of cancer. One of the main challenges is using\nmulti-omics data for identifying novel cancer driver genes. We\nhave developed an algorithm, called AMARETTO, that integrates\ncopy number, DNA methylation and gene expression data to\nidentify a set of driver genes by analyzing cancer samples and\nconnects them to clusters of co-expressed genes, which we\ndefine as modules. We applied AMARETTO in a pancancer setting\nto identify cancer driver genes and their modules on multiple\ncancer sites. AMARETTO captures modules enriched in\nangiogenesis, cell cycle and EMT, and modules that accurately\npredict survival and molecular subtypes. This allows AMARETTO\nto identify novel cancer driver genes directing canonical\ncancer pathways.", "License": "Apache License (== 2.0) + file LICENSE", "LazyLoad": "yes", "LazyData": "true", "Encoding": "UTF-8", "biocViews": "StatisticalMethod,DifferentialMethylation,GeneRegulation,GeneExpression,MethylationArray,Transcription,Preprocessing,BatchEffect,DataImport,mRNAMicroarray,MicroRNAArray,Regression,Clustering,RNASeq,CopyNumberVariation,Sequencing,Microarray,Normalization,Network,Bayesian,ExonArray,OneChannel,TwoChannel,ProprietaryPlatforms,AlternativeSplicing,DifferentialExpression,DifferentialSplicing,GeneSetEnrichment,MultipleComparison,QualityControl,TimeCourse", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-22 09:38:11 UTC", "User": "root" }, "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "6.1.1.9000", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibssl-dev perl libx11-dev zlib1g-dev", "Repository": 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