DOI: 10.18129/B9.bioc.MultiAssayExperiment    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see MultiAssayExperiment.

Software for the integration of multi-omics experiments in Bioconductor

Bioconductor version: 3.12

MultiAssayExperiment harmonizes data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.

Author: Marcel Ramos [aut, cre], Levi Waldron [aut], MultiAssay SIG [ctb]

Maintainer: Marcel Ramos <marcel.ramos at>

Citation (from within R, enter citation("MultiAssayExperiment")):


To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Coordinating Analysis of Multi-Assay Experiments
HTML R Script HDF5Array and MultiAssayExperiment
PDF MultiAssayExperiment_cheatsheet.pdf
HTML R Script Quick-start Guide
PDF   Reference Manual
Text   NEWS
Video   MultiAssayExperiment demo
Video   Marcel Ramos, Workshop 200: MultiAssayExperiment and curatedTCGAData Bioconductor 2020 workshop


biocViews DataRepresentation, Infrastructure, Software
Version 1.16.0
In Bioconductor since BioC 3.4 (R-3.3) (4.5 years)
License Artistic-2.0
Depends R (>= 4.0.0), SummarizedExperiment(>= 1.3.81)
Imports methods, GenomicRanges(>= 1.25.93), BiocGenerics, S4Vectors(>= 0.23.19), IRanges, Biobase, stats, tidyr, utils
Suggests BiocStyle, testthat, knitr, rmarkdown, R.rsp, HDF5Array, RaggedExperiment, UpSetR, survival, survminer
Depends On Me CAGEr, cBioPortalData, ClassifyR, curatedTCGAData, evaluomeR, glmSparseNet, hipathia, InTAD, missRows, OMICsPCAdata, QFeatures, SingleCellMultiModal, TimiRGeN, yriMulti
Imports Me AffiXcan, AMARETTO, animalcules, corral, ELMER, GOpro, HMP2Data, LinkHD, metabolomicsWorkbenchR, MOFA, MOMA, MultiBaC, netDx, OMICsPCA, omicsPrint, padma, scp, TCGAutils
Suggests Me BiocOncoTK, brgedata, CNVRanger, deco, MOFA2, MOFAdata, MultiDataSet, RaggedExperiment
Links To Me
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