MultiAssayExperiment

This is the development version of MultiAssayExperiment; for the stable release version, see MultiAssayExperiment.

Software for the integration of multi-omics experiments in Bioconductor

Bioconductor version: Development (3.19)

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] , 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 roswellpark.org>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MultiAssayExperiment")

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

Documentation


Reference Manual	PDF
MultiAssayExperiment demo	Video
Marcel Ramos, Workshop 200: MultiAssayExperiment and curatedTCGAData Bioconductor 2020 workshop	Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	1.29.1
In Bioconductor since	BioC 3.4 (R-3.3) (7.5 years)
License	Artistic-2.0
Depends	SummarizedExperiment(>= 1.3.81)
Imports	Biobase, BiocBaseUtils, BiocGenerics, DelayedArray, GenomicRanges(>= 1.25.93), IRanges, methods, S4Vectors(>= 0.23.19), stats, tidyr, utils
System Requirements
URL	http://waldronlab.io/MultiAssayExperiment/
Bug Reports	https://github.com/waldronlab/MultiAssayExperiment/issues

Suggests	BiocStyle, HDF5Array(>= 1.19.17), knitr, maftools(>= 2.7.10), R.rsp, RaggedExperiment, rmarkdown, survival, survminer, testthat, UpSetR
Linking To
Enhances
Depends On Me	alabaster.mae, CAGEr, cBioPortalData, ClassifyR, curatedPCaData, curatedTCGAData, evaluomeR, hipathia, InTAD, MGnifyR, mia, microbiomeDataSets, midasHLA, MIRit, missRows, OMICsPCAdata, QFeatures, scMultiome, SingleCellMultiModal, terraTCGAdata, TimiRGeN
Imports Me	AffiXcan, AMARETTO, animalcules, autonomics, biosigner, CoreGx, corral, curatedTBData, ELMER, FindIT2, FLAMES, gDRcore, gDRimport, gDRutils, glmSparseNet, GOpro, hermes, HMP2Data, LinkHD, metabolomicsWorkbenchR, MetaScope, MOMA, msqrob2, MuData, MultiBaC, MultimodalExperiment, netDx, nipalsMCIA, OMICsPCA, omicsPrint, padma, PDATK, PharmacoGx, phenomis, ropls, scp, scPipe, TCGAutils, TCGAWorkflow, vsclust, xcore
Suggests Me	BiocOncoTK, brgedata, CNVRanger, maftools, MOFA2, MOFAdata, MultiDataSet, RaggedExperiment, updateObject
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/MultiAssayExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MultiAssayExperiment
Package Short Url	https://bioconductor.org/packages/MultiAssayExperiment/
Package Downloads Report	Download Stats