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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

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

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 R (>= 3.5.0), 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
See More
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 MultiAssayExperiment_1.29.1.tar.gz
Windows Binary MultiAssayExperiment_1.29.1.zip
macOS Binary (x86_64) MultiAssayExperiment_1.29.1.tgz
macOS Binary (arm64) MultiAssayExperiment_1.29.1.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