Package: AMARETTO
Type: Package
Title: Regulatory Network Inference and Driver Gene Evaluation using
        Integrative Multi-Omics Analysis and Penalized Regression
Version: 1.25.0
Date: 2016-06-06
Author: Jayendra Shinde, Celine Everaert, Shaimaa Bakr, Mohsen Nabian, Jishu Xu,
	Vincent Carey, Nathalie Pochet and Olivier Gevaert
Maintainer: Olivier Gevaert <olivier.gevaert@gmail.com>
Depends: R (>= 3.6), impute, doParallel, grDevices, dplyr, methods,
        ComplexHeatmap
Description: Integrating an increasing number of available multi-omics cancer data remains one of the main challenges to improve our understanding of cancer. One of the main challenges is using multi-omics data for identifying  novel cancer driver genes. We have developed an algorithm, called AMARETTO, that integrates copy number, DNA methylation and gene expression data to identify a set of driver genes by analyzing cancer samples and connects them to clusters of co-expressed genes, which we define as modules. We applied AMARETTO in a pancancer setting to identify cancer driver genes and their modules on multiple cancer sites. AMARETTO captures modules enriched in angiogenesis, cell cycle and EMT, and modules that accurately predict survival and molecular subtypes. This allows AMARETTO to identify novel cancer driver genes directing canonical cancer 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
Suggests: testthat, MASS, knitr, BiocStyle
NeedsCompilation: no
Packaged: 2025-06-04 21:22:14 UTC; biocbuild
Imports: callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT,
        MultiAssayExperiment, circlize, curatedTCGAData, foreach,
        glmnet, httr, limma, matrixStats, readr, reshape2, tibble,
        rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2,
        gridExtra, utils
Roxygen: list(markdown = TRUE)
RoxygenNote: 6.1.1.9000
LinkingTo: Rcpp
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/AMARETTO
git_branch: devel
git_last_commit: 328c75f
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
Built: R 4.5.0; ; 2025-06-05 12:25:25 UTC; windows
