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Software for the integration of multi-omics experiments in Bioconductor

Bioconductor version: Release (3.19)

Harmonize 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] , Martin Morgan [aut, ctb], Lori Shepherd [ctb], Hervé Pagès [ctb], Vincent J Carey [aut, ctb], 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 "4.4") and enter:

if (!require("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:

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


biocViews DataRepresentation, Infrastructure, Software
Version 1.30.3
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License Artistic-2.0
Depends SummarizedExperiment(>= 1.3.81), R (>= 3.5.0)
Imports Biobase, BiocBaseUtils, BiocGenerics, DelayedArray, GenomicRanges, IRanges, methods, S4Vectors, tidyr, utils
System Requirements
Bug Reports
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Suggests BiocStyle, HDF5Array, knitr, maftools, R.rsp, RaggedExperiment, reshape2, rmarkdown, survival, survminer, testthat, UpSetR
Linking To
Depends On Me alabaster.mae, CAGEr, cBioPortalData, ClassifyR, evaluomeR, hipathia, InTAD, MGnifyR, mia, midasHLA, MIRit, missRows, QFeatures, terraTCGAdata, curatedPCaData, curatedTCGAData, microbiomeDataSets, OMICsPCAdata, scMultiome, SingleCellMultiModal
Imports Me AffiXcan, AMARETTO, animalcules, autonomics, biosigner, CoreGx, corral, ELMER, FindIT2, FLAMES, gDRcore, gDRimport, gDRutils, gINTomics, glmSparseNet, GOpro, hermes, LinkHD, metabolomicsWorkbenchR, MOMA, msqrob2, MuData, MultiBaC, MultimodalExperiment, nipalsMCIA, OMICsPCA, omicsPrint, padma, PDATK, PharmacoGx, phenomis, ropls, scp, scPipe, TCGAutils, vsclust, xcore, curatedTBData, HMP2Data, MetaScope, TCGAWorkflow, MOCHA
Suggests Me BiocOncoTK, CNVRanger, maftools, MOFA2, MultiDataSet, RaggedExperiment, updateObject, brgedata, MOFAdata, teal, teal.slice
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package MultiAssayExperiment_1.30.3.tar.gz
Windows Binary
macOS Binary (x86_64) MultiAssayExperiment_1.30.3.tgz
macOS Binary (arm64) MultiAssayExperiment_1.30.3.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive