Package: AMARETTO 1.29.0

Olivier Gevaert

AMARETTO: Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

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.

Authors:Jayendra Shinde, Celine Everaert, Shaimaa Bakr, Mohsen Nabian, Jishu Xu, Vincent Carey, Nathalie Pochet and Olivier Gevaert

AMARETTO_1.29.0.tar.gz
AMARETTO_1.29.0.zip(r-4.7)AMARETTO_1.29.0.zip(r-4.6)AMARETTO_1.29.0.zip(r-4.5)
AMARETTO_1.29.0.tgz(r-4.6-any)AMARETTO_1.29.0.tgz(r-4.5-any)
AMARETTO_1.29.0.tar.gz(r-4.7-any)AMARETTO_1.29.0.tar.gz(r-4.6-any)
AMARETTO_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
AMARETTO/json (API)
NEWS

# Install 'AMARETTO' in R:
install.packages('AMARETTO', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:AMARETTO-1.29.0(bioc 3.24)AMARETTO-1.28.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

statisticalmethoddifferentialmethylationgeneregulationgeneexpressionmethylationarraytranscriptionpreprocessingbatcheffectdataimportmrnamicroarraymicrornaarrayregressionclusteringrnaseqcopynumbervariationsequencingmicroarraynormalizationnetworkbayesianexonarrayonechanneltwochannelproprietaryplatformsalternativesplicingdifferentialexpressiondifferentialsplicinggenesetenrichmentmultiplecomparisonqualitycontroltimecourse

4.88 score 15 scripts 510 downloads 5 mentions 12 exports 139 dependencies

Last updated from:05ae352323. Checks:3 ERROR, 5 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR228
linux-devel-x86_64WARNING451
source / vignettesOK308
linux-release-x86_64WARNING432
macos-release-arm64ERROR314
macos-oldrel-arm64WARNING223
windows-develERROR1200
windows-releaseWARNING1326
windows-oldrelWARNING1240
wasm-releaseOK189

Exports:AMARETTO_CreateModuleDataAMARETTO_CreateRegulatorProgramsAMARETTO_DownloadAMARETTO_EvaluateTestSetAMARETTO_ExportResultsAMARETTO_HTMLreportAMARETTO_InitializeAMARETTO_PreprocessAMARETTO_RunAMARETTO_VisualizeModuleplot_run_historyread_gct

Dependencies:abindAnnotationDbiAnnotationHubaskpassbase64encBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocManagerBiocVersionBiostringsbitbit64blobbslibcachemcallrcirclizeclicliprclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncrosstalkcuratedTCGADatacurlDBIdbplyrDelayedArraydigestdir.expirydoParalleldplyrDTevaluateExperimentHubfarverfastmapfilelockfontawesomeforeachfsgenericsGenomicRangesGetoptLongggplot2glmnetGlobalOptionsgluegridExtragtableh5mreadHDF5Arrayhighrhmshtmltoolshtmlwidgetshttrhttr2imputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglaterlatticelazyevallifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeMultiAssayExperimentopensslotelpillarpkgconfigplyrpngprettyunitsprocessxprogresspromisespspurrrR6rappdirsRColorBrewerRcppRcppEigenreadrreshape2rhdf5rhdf5filtersRhdf5librjsonrlangrmarkdownRSQLiteS4ArraysS4VectorsS7sassscalesSeqinfoshapeSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunXVectoryaml

AMARETTO

Jayendra Shinde1, Celine Everaert2, Shaimaa Bakr1, Mohsen Nabian2, Jishu Xu2,Vincent Carey2, Nathalie Pochet2, Olivier Gevaert1**1 Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine and Biomedical Data Science, 1265 Welch Rd, Stanford, CA, USA 2 Brigham and Women's Hospital, Harvard Medical School, Broad Institute of MIT and Harvard, Boston and Cambridge, MA, USA [email protected] **[email protected]

Rendered fromamaretto.Rmdusingknitr::rmarkdownon May 22 2026.

Last update: 2022-12-27
Started: 2018-10-30