MultiAssayExperiment

Software for the integration of multi-omics experiments in Bioconductor

Bioconductor version: Release (3.20)

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 sph.cuny.edu>

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")

BiocManager::install("MultiAssayExperiment")

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

Documentation

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

browseVignettes("MultiAssayExperiment")

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
NEWS	Text
	Video
	Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	1.32.0
In Bioconductor since	BioC 3.4 (R-3.3) (8 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
URL	http://waldronlab.io/MultiAssayExperiment/
Bug Reports	https://github.com/waldronlab/MultiAssayExperiment/issues

Suggests	BiocStyle, HDF5Array, knitr, maftools, R.rsp, RaggedExperiment, reshape2, rmarkdown, survival, survminer, testthat, UpSetR
Linking To
Enhances
Depends On Me	alabaster.mae, CAGEr, cBioPortalData, ClassifyR, evaluomeR, hipathia, HoloFoodR, 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, gDRcore, gDRimport, gDRutils, gINTomics, glmSparseNet, GOpro, hermes, LinkHD, metabolomicsWorkbenchR, MOMA, MOSClip, msqrob2, MuData, MultiBaC, MultimodalExperiment, nipalsMCIA, OMICsPCA, omicsPrint, omXplore, padma, PharmacoGx, phenomis, ropls, scp, scPipe, survClust, TCGAutils, vsclust, xcore, curatedTBData, HMP2Data, LegATo, MetaScope, TCGAWorkflow, MOCHA
Suggests Me	CNVRanger, funOmics, maftools, MOFA2, MultiDataSet, RaggedExperiment, updateObject, brgedata, MOFAdata, teal, teal.slice
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	MultiAssayExperiment_1.32.0.tar.gz
Windows Binary (x86_64)	MultiAssayExperiment_1.32.0.zip
macOS Binary (x86_64)	MultiAssayExperiment_1.32.0.tgz
macOS Binary (arm64)	MultiAssayExperiment_1.31.5.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MultiAssayExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MultiAssayExperiment
Bioc Package Browser	https://code.bioconductor.org/browse/MultiAssayExperiment/
Package Short Url	https://bioconductor.org/packages/MultiAssayExperiment/
Package Downloads Report	Download Stats