Software For The Integration Of Multi-Omics Experiments In Bioconductor


We recommend installing the stable release version of MultiAssayExperiment in Bioconductor. This can be done using BiocManager:

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



Here is a visual overview of the MultiAssayExperiment class. The three main components are:

  • colData - phenotype data
  • ExperimentList - a list of tables from experimental results
  • sampleMap - a graph representation of ‘samples’ and ‘participants’

Note. For simplicity, we use the terms ‘samples’ and ‘participants’ to elucidate the relationship although MultiAssayExperiment can work on other biological specimens.

MultiAssayExperiment schematic

MultiAssayExperiment schematic


Ready-to-use MultiAssayExperiment objects

For easy-to-use and ready-made MultiAssayExperiment objects, use the curatedTCGAData experiment data package.


Companion package for working with TCGA data

TCGAutils is a handy package for working with MultiAssayExperiment data objects from curatedTCGAData. It is highly recommended to use TCGAutils for identifier manipulation, sample identification and more.



The MultiAssayExperiment API is available by browsing to the API wiki.

The MultiAssayExperiment Bioconductor Special Interest Group

This group meets remotely to discuss this project approximately every 3 weeks. If you are interested, please join the MultiAssayExperiment Google Group and see the calendar of upcoming meetings.

Contributor Code of Conduct

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This Code of Conduct is adapted from the Contributor Covenant, version 1.0.0, available at